High throughput screening assay systems in microscale fluidic devices

ABSTRACT

The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays. In particular, the devices and methods of the invention are useful in screening large numbers of different compounds for their effects on a variety of chemical, and preferably, biochemical systems.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is a continuation of U.S. patent application Ser. No. 10/279,496filed Oct. 24, 2002, which is a continuation of U.S. patent applicationSer. No. 09/132,963 filed Aug. 12, 1998, now U.S. Pat. No. 6,479,299,which is a continuation of U.S. patent application Ser. No. 08/881,696filed Jun. 24, 1997, now U.S. Pat. No. 6,267,858, which is acontinuation-in-part of U.S. patent application Ser. No. 08/671,987filed Jun. 28, 1996, now U.S. Pat. No. 5,942,443, and U.S. patentapplication Ser. No. 08/761,575 filed Dec. 6, 1996, now U.S. Pat. No.6,046,056 each of which is hereby incorporated herein by reference inits entirety for all purposes. A PCT Application designating the UnitedStates of America, WO 98/00231, International Application No.PCT/US97/10894 substantially identical to the present application wasco-filed in the United States Receiving Office on Jun. 24, 1997. Thisapplication is also incorporated herein by reference.

FIELD OF THE INVENTION

This application relates to apparatus and assay systems for detectingmolecular interactions. The apparatus comprise a substrate with one ormore intersecting channels and an electroosmotic fluid movementcomponent, or other component for moving fluid in the channels on thesubstrate.

BACKGROUND OF THE INVENTION

There has long been a need for the ability to rapidly assay compoundsfor their effects on various biological processes. For example,enzymologists have long sought better substrates, better inhibitors orbetter catalysts for enzymatic reactions. Similarly, in thepharmaceutical industries, attention has been focused on identifyingcompounds that may block, reduce, or even enhance the interactionsbetween biological molecules. Specifically, in biological systems theinteraction between a receptor and its ligand often may result, eitherdirectly or through some downstream event, in either a deleterious orbeneficial effect on that system, and consequently, on a patient forwhom treatment is sought. Accordingly, researchers have long soughtafter compounds or mixtures of compounds that can reduce, block or evenenhance that interaction. Similarly, the ability to rapidly processsamples for detection of biological molecules relevant to diagnostic orforensic analysis is of fundamental value for, e.g., diagnosticmedicine, archaeology, anthropology, and modern criminal investigation.

Modern drug discovery is limited by the throughput of the assays thatare used to screen compounds that possess these described effects. Inparticular, screening of a maximum number of different compoundsnecessitates reducing the time and labor requirements associated witheach screen.

High throughput screening of collections of chemically synthesizedmolecules and of natural products (such as microbial fermentationbroths) has thus played a central role in the search for lead compoundsfor the development of new pharmacological agents. The remarkable surgeof interest in combinatorial chemistry and the associated technologiesfor generating and evaluating molecular diversity represent significantmilestones in the evolution of this paradigm of drug discovery. SeePavia et al., 1993, Bioorg. Med. Chem. Lett. 3: 387–396, incorporatedherein by reference. To date, peptide chemistry has been the principlevehicle for exploring the utility of combinatorial methods in ligandidentification. See Jung & Beck-Sickinger, 1992, Angew. Chem. Int. Ed.Engl. 31: 367–383, incorporated herein by reference. This may beascribed to the availability of a large and structurally diverse rangeof amino acid monomers, a relatively generic, high-yielding solid phasecoupling chemistry and the synergy with biological approaches forgenerating recombinant peptide libraries. Moreover, the potent andspecific biological activities of many low molecular weight peptidesmake these molecules attractive starting points for therapeutic drugdiscovery. See Hirschmann, 1991, Angew. Chem. Int. Ed. Engl. 30:1278–1301, and Wiley & Rich, 1993, Med. Res. Rev. 13: 327–384, each ofwhich is incorporated herein by reference. Unfavorable pharmacodynamicproperties such as poor oral bioavailability and rapid clearance in vivohave limited the more widespread development of peptidic compounds asdrugs, however. This realization has recently inspired workers to extendthe concepts of combinatorial organic synthesis beyond peptide chemistryto create libraries of known pharmacophores like benzodiazepines (seeBunin & Ellman, 1992, J. Amer. Chem. Soc. 114: 10997–10998, incorporatedherein by reference) as well as polymeric molecules such as oligomericN-substituted glycines (“peptoids”) and oligocarbamates. See Simon etal., 1992, Proc. Natl. Acad. Sci. USA 89: 9367–9371; Zuckermann et al.,1992, J. Amer. Chem. Soc. 114: 10646–10647; and Cho et al., 1993,Science 261:1303–1305, each of which is incorporated herein byreference.

In similar developments, much as modern combinatorial chemistry hasresulted in a dramatic increase in the number of test compounds that maybe screened, human genome research has also uncovered large numbers ofnew target molecules (e.g., genes and gene products such as proteins andRNA) against which the efficacy of test compounds are screened.

Despite the improvements achieved using parallel screening methods andother technological advances, such as robotics and high throughputdetection systems, current screening methods still have a number ofassociated problems. For example, screening large numbers of samplesusing existing parallel screening methods have high space requirementsto accommodate the samples and equipment, e.g., robotics, etc., highcosts associated with that equipment, and high reagent requirementsnecessary for performing the assays. Additionally, in many cases,reaction volumes must be very small to account for the small amounts ofthe test compounds that are available. Such small volumes compounderrors associated with fluid handling and measurement, e.g., due toevaporation, small dispensing errors, or the like. Additionally, fluidhandling equipment and methods have typically been unable to handlethese volume ranges with any acceptable level of accuracy due in part tosurface tension effects in such small volumes.

The development of systems to address these problems must consider avariety of aspects of the assay process. Such aspects include target andcompound sources, test compound and target handling, specific assayrequirements, and data acquisition, reduction storage and analysis. Inparticular, there exists a need for high throughput screening methodsand associated equipment and devices that are capable of performingrepeated, accurate assay screens, and operating at very small volumes.

The present invention meets these and a variety of other needs. Inparticular, the present invention provides novel methods and apparatusesfor performing screening assays which address and provide meaningfulsolutions to these problems.

SUMMARY OF THE INVENTION

The present invention provides methods of screening a plurality of testcompounds for an effect on a biochemical system. These methods typicallyutilize microfabricated substrates which have at least a first surface,and at least two intersecting channels fabricated into that firstsurface. At least one of the intersecting channels will have at leastone cross-sectional dimension in a range from 0.1 to 500 μm. The methodsinvolve flowing a first component of a biochemical system in a first ofthe at least two intersecting channels. At least a first test compoundis flowed from a second channel into the first channel whereby the testcompound contacts the first component of the biochemical system. Aneffect of the test compound on the biochemical system is then detected.

In a related aspect, the method comprises continuously flowing the firstcomponent of a biochemical system in the first channel of the at leasttwo intersecting channels. Different test compounds are periodicallyintroduced into the first channel from a second channel. The effect, ifany, of the test compound on the biochemical system is then detected.

In an alternative aspect, the methods utilize a substrate having atleast a first surface with a plurality of reaction channels fabricatedinto the first surface. Each of the plurality of reaction channels isfluidly connected to at least two transverse channels also fabricated inthe surface. The at least first component of a biochemical system isintroduced into the plurality of reaction channels, and a plurality ofdifferent test compounds is flowed through at least one of the at leasttwo transverse channels. Further, each of the plurality of testcompounds is introduced into the transverse channel in a discretevolume. Each of the plurality of different test compounds is directedinto a separate reaction channel and the effect of each of the testcompounds on the biochemical system is then detected.

The present invention also provides apparatuses for practicing the abovemethods. In one aspect, the present invention provides an apparatus forscreening test compounds for an effect on a biochemical system. Thedevice comprises a substrate having at least one surface with at leasttwo intersecting channels fabricated into the surface. The at least twointersecting channels have at least one cross-sectional dimension in therange from about 0.1 to about 500 μm. The device also comprises a sourceof different test compounds fluidly connected to a first of the at leasttwo intersecting channels, and a source of at least one component of thebiochemical system fluidly connected to a second of the at least twointersecting channels. Also included are fluid direction systems forflowing the at least one component within the intersecting channels, andfor introducing the different test compounds from the first to thesecond of the intersecting channels. The apparatus also optionallycomprises a detection zone in the second channel for detecting an effectof said test compound on said biochemical system.

In preferred aspects, the apparatus of the invention includes a fluiddirection system which comprises at least three electrodes, eachelectrode being in electrical contact with the at least two intersectingchannels on a different side of an intersection formed by the at leasttwo intersecting channels. The fluid direction system also includes acontrol system for concomitantly applying a variable voltage at each ofthe electrodes, whereby movement of the test compounds or the at leastfirst component in the at least two intersecting channels arecontrolled.

In another aspect, the present invention provides an apparatus fordetecting an effect of a test compound on a biochemical system,comprising a substrate having at least one surface with a plurality ofreaction channels fabricated into the surface. The apparatus also has atleast two transverse channels fabricated into the surface, wherein eachof the plurality of reaction channels is fluidly connected to a first ofthe at least two transverse channels at a first point in each of thereaction channels, and fluidly connected to a second transverse channelat a second point in each of the reaction channels. The apparatusfurther includes a source of at least one component of the biochemicalsystem fluidly connected to each of the reaction channels, a source oftest compounds fluidly connected to the first of the transversechannels, and a fluid direction system for controlling movement of thetest compound and the first component within the transverse channels andthe plurality of reaction channels. As above, the apparatuses alsooptionally include a detection zone in the second transverse channel fordetecting an effect of the test compound on the biochemical system.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of one embodiment of amicrolaboratory screening assay system of the present invention whichcan be used in running a continuous flow assay system.

FIGS. 2A and 2B show a schematic illustration of the apparatus shown inFIG. 1, operating in alternate assay systems. FIG. 2A shows a systemused for screening effectors of an enzyme-substrate interaction. FIG. 2Billustrates the use of the apparatus in screening effectors ofreceptor-ligand interactions.

FIG. 3 is a schematic illustration of a “serial input parallel reaction”microlaboratory assay system in which compounds to be screened areserially introduced into the device but then screened in a parallelorientation within the device.

FIGS. 4A–4F show a schematic illustration of the operation of the deviceshown in FIG. 3, in screening a plurality of bead based test compounds.

FIG. 5 shows a schematic illustration of a continuous flow assay deviceincorporating a sample shunt for performing prolonged incubationfollowed by a separation step.

FIG. 6A shows a schematic illustration of a serial input parallelreaction device for use with fluid based test compounds. FIGS. 6B and 6Cshow a schematic illustration of fluid flow patterns within the deviceshown in FIG. 6A.

FIG. 7 shows a schematic illustration of one embodiment of an overallassay system which employs multiple microlaboratory devices labeled as“LabChip®” for screening test compounds.

FIG. 8 is a schematic illustration of a chip layout used for acontinuous-flow assay screening system.

FIGS. 9A and 9B show fluorescence data from a continuous flow assayscreen. FIG. 9A shows fluorescence data from a test screen whichperiodically introduced a known inhibitor (IPTG) into a β-galactosidaseassay system in a chip format. FIG. 9B shows a superposition of two datasegments from FIG. 9A, directly comparing the inhibitor data withcontrol (buffer) data.

FIG. 10 illustrates the operating parameters of a fluid flow system on asmall chip device for performing enzyme inhibitor screening.

FIG. 11 shows a schematic illustration of timing for sample/spacerloading in a microfluidic device channel.

FIG. 12, panels A–G schematically illustrate electrodes used inapparatuses of the invention.

DESCRIPTION OF THE PREFERRED EMBODIMENT

I. Applications for the Invention

The present invention provides novel microlaboratory systems and methodsthat are useful for performing high-throughput screening assays. Inparticular, the present invention provides microfluidic devices andmethods of using such devices in screening large numbers of differentcompounds for their effects on a variety of chemical, and preferably,biochemical systems.

As used herein, the phrase “biochemical system” generally refers to achemical interaction that involves molecules of the type generally foundwithin living organisms. Such interactions include the full range ofcatabolic and anabolic reactions which occur in living systems includingenzymatic, binding, signalling and other reactions. Further, biochemicalsystems, as defined herein, also include model systems which are mimeticof a particular biochemical interaction. Examples of biochemical systemsof particular interest in practicing the present invention include,e.g., receptor-ligand interactions, enzyme-substrate interactions,cellular signaling pathways, transport reactions involving model barriersystems (e.g., cells or membrane fractions) for bioavailabilityscreening, and a variety of other general systems. Cellular ororganismal viability or activity may also be screened using the methodsand apparatuses of the present invention, e.g., in toxicology studies.Biological materials which are assayed include, but are not limited to,cells, cellular fractions (membranes, cytosol preparations, etc.),agonists and antagonists of cell membrane receptors (e.g., cellreceptor-ligand interactions such as e.g., transferrin, c-kit, viralreceptor ligands (e.g., CD4-HIV), cytokine receptors, chemokinereceptors, interleukin receptors, immunoglobulin receptors andantibodies, the cadherein family, the integrin family, the selectinfamily, and the like; see, e.g., Pigott and Power (1993) The AdhesionMolecule FactsBook Academic Press New York and Hulme (ed) ReceptorLigand Interactions A Practical Approach Rickwood and Hames (serieseditors) IRL Press at Oxford Press NY), toxins and venoms, viralepitopes, hormones (e.g., opiates, steroids, etc.), intracellularreceptors (e.g. which mediate the effects of various small ligands,including steroids, thyroid hormone, retinoids and vitamin D; forreviews see, e.g., Evans (1988) Science, 240:889–895; Ham and Parker(1989) Curr. Opin. Cell Biol., 1:503–511; Burnstein et al. (1989), Ann.Rev. Physiol., 51:683–699; Truss and Beato (1993) Endocr. Rev.,14:459479), peptides, retro-inverso peptides, polymers of α-, β-, orω-amino acids (D- or L-), enzymes, enzyme substrates, cofactors, drugs,lectins, sugars, nucleic acids (both linear and cyclic polymerconfigurations), oligosaccharides, proteins, phospholipids andantibodies. Synthetic polymers such as heteropolymers in which a knowndrug is covalently bound to any of the above, such as polyurethanes,polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines,polyarylene sulfides, polysiloxanes, polyimides, and polyacetates arealso assayed. Other polymers are also assayed using the systemsdescribed herein, as would be apparent to one of skill upon review ofthis disclosure. One of skill will be generally familiar with thebiological literature. For a general introduction to biological systems,see, Berger and Kimmel, Guide to Molecular Cloning Techniques, Methodsin Enzymology volume 152 Academic Press, Inc., San Diego, Calif.(Berger); Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual(2nd ed.) Vol. 1–3, Cold Spring Harbor Laboratory, Cold Spring HarborPress, NY, (Sambrook); Current Protocols in Molecular Biology, F. M.Ausubel et al., eds., Current Protocols, a joint venture between GreenePublishing Associates, Inc. and John Wiley & Sons, Inc., (through 1997Supplement) (Ausubel); Watson et al. (1987) Molecular Biology of theGene, Fourth Edition The Benjamin/Cummings Publishing Co., Menlo Park,Calif.; Watson et al. (1992) Recombinant DNA Second Edition ScientificAmerican Books, NY; Alberts et al. (1989) Molecular Biology of the CellSecond Edition Garland Publishing, NY; Pattison (1994) Principles andPractice of Clinical Virology; Darnell et al., (1990) Molecular CellBiology second edition, Scientific American Books, W. H. Freeman andCompany; Berkow (ed.) The Merck Manual of Diagnosis and Therapy, Merck &Co., Rahway, N.J.; Harrison's Principles of Internal Medicine,Thirteenth Edition, Isselbacher et al. (eds). (1994) Lewin Genes, 5thEd., Oxford University Press (1994); The “Practical Approach” Series ofBooks (Rickwood and Hames (series eds.) by IRL Press at OxfordUniversity Press, NY; The “FactsBook Series” of books from AcademicPress, NY; Product information from manufacturers of biological reagentsand experimental equipment also provide information useful in assayingbiological systems. Such manufacturers include, e.g., the SIGMA chemicalcompany (Saint Louis, Mo.), R&D systems (Minneapolis, Minn.), PharmaciaLKB Biotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (PaloAlto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee,Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc.(Gaithersberg, Md.), Fluka Chemica-Biochemika Analytika (Fluka ChemieAG, Buchs, Switzerland), Invitrogen, San Diego, Calif., and AppliedBiosystems (Foster City, Calif.), as well as many other commercialsources known to one of skill.

In order to provide methods and devices for screening compounds foreffects on biochemical systems, the present invention generallyincorporates model in vitro systems which mimic a given biochemicalsystem in vivo for which effector compounds are desired. The range ofsystems against which compounds can be screened and for which effectorcompounds are desired, is extensive. For example, compounds areoptionally screened for effects in blocking, slowing or otherwiseinhibiting key events associated with biochemical systems whose effectis undesirable. For example, test compounds are optionally screened fortheir ability to block systems that are responsible, at least in part,for the onset of disease or for the occurrence of particular symptoms ofdiseases, including, e.g., hereditary diseases, cancer, bacterial orviral infections and the like. Compounds which show promising results inthese screening assay methods can then be subjected to further testingto identify effective pharmacological agents for the treatment ofdisease or symptoms of a disease.

Alternatively, compounds can be screened for their ability to stimulate,enhance or otherwise induce biochemical systems whose function isbelieved to be desirable, e.g., to remedy existing deficiencies in apatient.

Once a model system is selected, batteries of test compounds can then beapplied against these model systems. By identifying those test compoundsthat have an effect on the particular biochemical system, in vitro, onecan identify potential effectors of that system, in vivo.

In their simplest forms, the biochemical system models employed in themethods and apparatuses of the present invention will screen for aneffect of a test compound on an interaction between two components of abiochemical system, e.g., receptor-ligand interaction, enzyme-substrateinteraction, and the like. In this form, the biochemical system modelwill typically include the two normally interacting components of thesystem for which an effector is sought, e.g., the receptor and itsligand or the enzyme and its substrate.

Determining whether a test compound has an effect on this interactionthen involves contacting the system with the test compound and assayingfor the functioning of the system, e.g., receptor-ligand binding orsubstrate turnover. The assayed function is then compared to a control,e.g., the same reaction in the absence of the test compound or in thepresence of a known effector. Typically, such assays involve themeasurement of a parameter of the biochemical system. By “parameter ofthe biochemical system” is meant some measurable evidence of thesystem's functioning, e.g., the presence or absence of a labeled groupor a change in molecular weight (e.g., in binding reactions, transportscreens), the presence or absence of a reaction product or substrate (insubstrate turnover measurements), or an alteration in electrophoreticmobility (typically detected by a change in elution time of a labeledcompound).

Although described in terms of two-component biochemical systems, themethods and apparatuses may also be used to screen for effectors of muchmore complex systems, where the result or end product of the system isknown and assayable at some level, e.g., enzymatic pathways, cellsignaling pathways and the like. Alternatively, the methods andapparatuses described herein are optionally used to screen for compoundsthat interact with a single component of a biochemical system, e.g.,compounds that specifically bind to a particular biochemical compound,e.g., a receptor, ligand, enzyme, nucleic acid, structuralmacromolecule, etc.

Biochemical system models may also be embodied in whole cell systems.For example, where one is seeking to screen test compounds for an effecton a cellular response, whole cells are optionally utilized. Modifiedcell systems may also be employed in the screening systems encompassedherein. For example, chimeric reporter systems are optionally employedas indicators of an effect of a test compound on a particularbiochemical system. Chimeric reporter systems typically incorporate aheterogenous reporter system integrated into a signaling pathway whichsignals the binding of a receptor to its ligand. For example, a receptoris fused to a heterologous protein, e.g., an enzyme whose activity isreadily assayable. Activation of the receptor by ligand binding thenactivates the heterologous protein which then allows for detection.Thus, the surrogate reporter system produces an event or signal which isreadily detectable, thereby providing an assay for receptor/ligandbinding. Examples of such chimeric reporter systems have been previouslydescribed in the art.

Additionally, where one is screening for bioavailability, e.g.,transport, biological barriers are optionally included. The term“biological barriers” generally refers to cellular or membranous layerswithin biological systems, or synthetic models thereof. Examples of suchbiological barriers include the epithelial and endothelial layers, e.g.vascular endothelia and the like.

Biological responses are often triggered and/or controlled by thebinding of a receptor to its ligand. For example, interaction of growthfactors, i.e., epidermal growth factor (EGF), fibroblast growth factor(FGF), platelet-derived growth factor (PDGF), etc., with their receptorsstimulates a wide variety of biological responses including, e.g., cellproliferation and differentiation, activation of mediating enzymes,stimulation of messenger turnover, alterations in ion fluxes, activationof enzymes, changes in cell shape and the alteration in geneticexpression levels. Accordingly, control of the interaction of thereceptor and its ligand may offer control of the biological responsescaused by that interaction.

Accordingly, in one aspect, the present invention will be useful inscreening for compounds that affect an interaction between a receptormolecule and its ligands. As used herein, the term “receptor” generallyrefers to one member of a pair of compounds which specifically recognizeand bind to each other. The other member of the pair is termed a“ligand.” Thus, a receptor/ligand pair may include a typical proteinreceptor, usually membrane associated, and its natural ligand, e.g.,another protein or small molecule. Receptor/ligand pairs may alsoinclude antibody/antigen binding pairs, complementary nucleic acids,nucleic acid associating proteins and their nucleic acid ligands. Alarge number of specifically associating biochemical compounds are wellknown in the art and can be utilized in practicing the presentinvention.

Traditionally, methods for screening for effectors of a receptor/ligandinteraction have involved incubating a receptor/ligand binding pair inthe presence of a test compound. The level of binding of thereceptor/ligand pair is then compared to negative and/or positivecontrols. Where a decrease in normal binding is seen, the test compoundis determined to be an inhibitor of the receptor/ligand binding. Wherean increase in that binding is seen, the test compound is determined tobe an enhancer or inducer of the interaction.

In the interest of efficiency, screening assays have typically been setup in multiwell reaction plates, e.g., multi-well microplates, whichallow for the simultaneous, parallel screening of large numbers of testcompounds.

A similar, and perhaps overlapping, set of biochemical systems includesthe interactions between enzymes and their substrates. The term “enzyme”as used herein, generally refers to a protein which acts as a catalystto induce a chemical change in other compounds or “substrates.”

Typically, effectors of an enzyme's activity toward its substrate arescreened by contacting the enzyme with a substrate in the presence andabsence of the compound to be screened and under conditions optimal fordetecting changes in the enzyme's activity. After a set time forreaction, the mixture is assayed for the presence of reaction productsor a decrease in the amount of substrate. The amount of substrate thathas been catalyzed is them compared to a control, i.e., enzyme contactedwith substrate in the absence of test compound or presence of a knowneffector. As above, a compound that reduces the enzymes activity towardits substrate is termed an “inhibitor,” whereas a compound thataccentuates that activity is termed an “inducer.”

Generally, the various screening methods encompassed by the presentinvention involve the serial introduction of a plurality of testcompounds into a microfluidic device. Once injected into the device, thetest compound is screened for effect on a biological system using acontinuous serial or parallel assay orientation.

As used herein, the term “test compound” refers to the collection ofcompounds that are to be screened for their ability to affect aparticular biochemical system. Test compounds may include a wide varietyof different compounds, including chemical compounds, mixtures ofchemical compounds, e.g., polysaccharides, small organic or inorganicmolecules, biological macromolecules, e.g., peptides, proteins, nucleicacids, or an extract made from biological materials such as bacteria,plants, fungi, or animal cells or tissues, naturally occurring orsynthetic compositions. Depending upon the particular embodiment beingpracticed, the test compounds are provided, e.g., injected, free insolution, or are optionally attached to a carrier, or a solid support,e.g., beads. A number of suitable solid supports are employed forimmobilization of the test compounds. Examples of suitable solidsupports include agarose, cellulose, dextran (commercially available as,i.e., Sephadex, Sepharose) carboxymethyl cellulose, polystyrene,polyethylene glycol (PEG), filter paper, nitrocellulose, ion exchangeresins, plastic films, glass beads, polyaminemethylvinylether maleicacid copolymer, amino acid copolymer, ethylene-maleic acid copolymer,nylon, silk, etc. Additionally, for the methods and apparatusesdescribed herein, test compounds are screened individually, or ingroups. Group screening is particularly useful where hit rates foreffective test compounds are expected to be low such that one would notexpect more than one positive result for a given group. Alternatively,such group screening is used where the effects of different testcompounds are differentially detected in a single system, e.g., throughelectrophoretic separation of the effects, or differential labellingwhich enables separate detection.

Test compounds are commercially available, or derived from any of avariety of biological sources apparent to one of skill and as described,supra. In one aspect, a tissue homogenate or blood sample from a patientis tested in the assay systems of the invention. For example, in oneaspect, blood is tested for the presence or activity of a biologicallyrelevant molecule. For example, the presence and activity level of anenzyme are detected by supplying and enzyme substrate to the biologicalsample and detecting the formation of a product using an assay systemsof the invention. Similarly, the presence of infectious pathogens(viruses, bacteria, fungi, or the like) or cancerous tumors can betested by monitoring binding of a labeled ligand to the pathogen ortumor cells, or a component of the pathogen or tumor such as a protein,cell membrane, cell extract or the like, or alternatively, by monitoringthe presence of an antibody against the pathogen or tumor in thepatient's blood. For example, the binding of an antibody from apatient's blood to a viral protein such as an HIV protein is a commontest for monitoring patient exposure to the virus. Many assays fordetecting pathogen infection are well known, and are adapted to theassay systems of the present invention.

Biological samples are derived from patients using well known techniquessuch as venipuncture or tissue biopsy. Where the biological material isderived from non-human animals, such as commercially relevant livestock,blood and tissue samples are conveniently obtained from livestockprocessing plants. Similarly, plant material used in the assays of theinvention are conveniently derived from agricultural or horticulturalsources. Alternatively, a biological sample can be from a cell or bloodbank where tissue and/or blood are stored, or from an in vitro sourcesuch as a culture of cells. Techniques and methods for establishing aculture of cells for use as a source for biological materials are wellknown to those of skill in the art. Freshney Culture of Animal Cells, aManual of Basic Technique, Third Edition Wiley-Liss, New York (1994)provides a general introduction to cell culture.

II. Assay Systems

As described above, the screening methods of the present invention aregenerally carried out in microfluidic devices or “microlaboratorysystems,” which allow for integration of the elements required forperforming the assay, automation, and minimal environmental effects onthe assay system, e.g., evaporation, contamination, human error, or thelike. A number of devices for carrying out the assay methods of theinvention are described in substantial detail below. However, it will berecognized that the specific configuration of these devices willgenerally vary depending upon the type of assay and/or assay orientationdesired. For example, in some embodiments, the screening methods of theinvention can be carried out using a microfluidic device having twointersecting channels. For more complex assays or assay orientations,multichannel/intersection devices are optionally employed. The smallscale, integratability and self-contained nature of these devices allowsfor virtually any assay orientation to be realized within the context ofthe microlaboratory system.

A. Electrokinetic Material Transport

In preferred aspects, the devices, methods and systems described herein,employ electrokinetic material transport systems, and preferably,controlled electrokinetic material transport systems. As used herein,“electrokinetic material transport systems” include systems whichtransport and direct materials within an interconnected channel and/orchamber containing structure, through the application of electricalfields to the materials, thereby causing material movement through andamong the channel and/or chambers, i.e., cations will move toward thenegative electrode, while anions will move toward the positiveelectrode.

Such electrokinetic material transport and direction systems includethose systems that rely upon the electrophoretic mobility of chargedspecies within the electric field applied to the structure. Such systemsare more particularly referred to as electrophoretic material transportsystems. Other electrokinetic material direction and transport systemsrely upon the electroosmotic flow of fluid and material within a channelor chamber structure which results from the application of an electricfield across such structures. In brief, when a fluid is placed into achannel which has a surface bearing charged functional groups, e.g.,hydroxyl groups in etched glass channels or glass microcapillaries,those groups can ionize. In the case of hydroxyl functional groups, thisionization, e.g., at neutral pH, results in the release of protons fromthe surface and into the fluid, creating a concentration of protons atnear the fluid/surface interface, or a positively charged sheathsurrounding the bulk fluid in the channel. Application of a voltagegradient across the length of the channel, will cause the proton sheath,as well as the fluid it surrounds, to move in the direction of thevoltage drop, i.e., toward the negative electrode.

“Controlled electrokinetic material transport and direction,” as usedherein, refers to electrokinetic systems as described above, whichemploy active control of the voltages applied at multiple, i.e., morethan two, electrodes. Rephrased, such controlled electrokinetic systemsconcomitantly regulate voltage gradients applied across at least twointersecting channels. Controlled electrokinetic material transport isdescribed in Published PCT Application No. WO 96/04547, to Ramsey, whichis incorporated herein by reference in its entirety for all purposes. Inparticular, the preferred microfluidic devices and systems describedherein, include a body structure which includes at least twointersecting channels or fluid conduits, e.g., interconnected, enclosedchambers, which channels include at least three unintersected termini.The intersection of two channels refers to a point at which two or morechannels are in fluid communication with each other, and encompasses “T”intersections, cross intersections, “wagon wheel” intersections ofmultiple channels, or any other channel geometry where two or morechannels are in such fluid communication. An unintersected terminus of achannel is a point at which a channel terminates not as a result of thatchannel's intersection with another channel, e.g., a “T” intersection.In preferred aspects, the devices will include at least threeintersecting channels having at least four unintersected termini. In abasic cross channel structure, where a single horizontal channel isintersected and crossed by a single vertical channel, controlledelectrokinetic material transport operates to controllably directmaterial flow through the intersection, by providing constraining flowsfrom the other channels at the intersection. For example, assuming onewas desirous of transporting a first material through the horizontalchannel, e.g., from left to right, across the intersection with thevertical channel. Simple electrokinetic material flow of this materialacross the intersection could be accomplished by applying a voltagegradient across the length of the horizontal channel, i.e., applying afirst voltage to the left terminus of this channel, and a second, lowervoltage to the right terminus of this channel, or by allowing the rightterminus to float (applying no voltage). However, this type of materialflow through the intersection would result in a substantial amount ofdiffusion at the intersection, resulting from both the natural diffusiveproperties of the material being transported in the medium used, as wellas convective effects at the intersection.

In controlled electrokinetic material transport, the material beingtransported across the intersection is constrained by low level flowfrom the side channels, e.g., the top and bottom channels. This isaccomplished by applying a slight voltage gradient along the path ofmaterial flow, e.g., from the top or bottom termini of the verticalchannel, toward the right terminus. The result is a “pinching” of thematerial flow at the intersection, which prevents the diffusion of thematerial into the vertical channel. The pinched volume of material atthe intersection may then be injected into the vertical channel byapplying a voltage gradient across the length of the vertical channel,i.e., from the top terminus to the bottom terminus. In order to avoidany bleeding over of material from the horizontal channel during thisinjection, a low level of flow is directed back into the side channels,resulting in a “pull back” of the material from the intersection.

In addition to pinched injection schemes, controlled electrokineticmaterial transport is readily utilized to create virtual valves whichinclude no mechanical or moving parts. Specifically, with reference tothe cross intersection described above, flow of material from onechannel segment to another, e.g., the left arm to the right arm of thehorizontal channel, can be efficiently regulated, stopped andreinitiated, by a controlled flow from the vertical channel, e.g., fromthe bottom arm to the top arm of the vertical channel. Specifically, inthe ‘off’ mode, the material is transported from the left arm, throughthe intersection and into the top arm by applying a voltage gradientacross the left and top termini. A constraining flow is directed fromthe bottom arm to the top arm by applying a similar voltage gradientalong this path (from the bottom terminus to the top terminus). Meteredamounts of material are then dispensed from the left arm into the rightarm of the horizontal channel by switching the applied voltage gradientfrom left to top, to left to right. The amount of time and the voltagegradient applied dictates the amount of material that will be dispensedin this manner. Although described for the purposes of illustration withrespect to a four way, cross intersection, these controlledelectrokinetic material transport systems can be readily adapted formore complex interconnected channel networks, e.g., arrays ofinterconnected parallel channels.

B. Continuous Flow Assay Systems

In one preferred aspect, the methods and apparatuses of the inventionare used in screening test compounds using a continuous flow assaysystem. Generally, the continuous flow assay system can be readily usedin screening for inhibitors or inducers of enzymatic activity, or foragonists or antagonists of receptor-ligand binding. In brief, thecontinuous flow assay system involves the continuous flow of theparticular biochemical system along a microfabricated channel. As usedherein, the term “continuous” generally refers to an unbroken orcontiguous stream of the particular composition that is beingcontinuously flowed. For example, a continuous flow may include aconstant fluid flow having a set velocity, or alternatively, a fluidflow which includes pauses in the flow rate of the overall system, suchthat the pause does not otherwise interrupt the flow stream. Thefunctioning of the system is indicated by the production of a detectableevent or signal. In one preferred embodiment, such detectable signalsinclude optically detectable chromophoric or fluorescent signals thatare associated with the functioning of the particular model system used.For enzyme systems, such signals will generally be produced by productsof the enzyme's catalytic action, e.g., on a chromogenic or fluorogenicsubstrate. For binding systems, e.g., receptor ligand interactions,signals will typically involve the association of a labeled ligand withthe receptor, or vice versa.

A wide variety of other detectable signals and labels can also be usedin the assays and apparatuses of the invention. In addition to thechromogenic and fluorogenic labels described above, radioactive decay,electron density, changes in pH, solvent viscosity, temperature and saltconcentration are also conveniently measured.

More generally, labels are commonly detectable by spectroscopic,photochemical, biochemical, immunochemical, or chemical means. Forexample, useful nucleic acid labels include 32P, 35S, fluorescent dyes,electron-dense reagents, enzymes (e.g., as commonly used in an ELISA),biotin, dioxigenin, or haptens and proteins for which antisera ormonoclonal antibodies are available. A wide variety of labels suitablefor labeling biological components are known and are reportedextensively in both the scientific and patent literature, and aregenerally applicable to the present invention for the labeling ofbiological components. Suitable labels include radionucleotides,enzymes, substrates, cofactors, inhibitors, fluorescent moieties,chemiluminescent moieties, magnetic particles, and the like. Labelingagents optionally include e.g., monoclonal antibodies, polyclonalantibodies, proteins, or other polymers such as affinity matrices,carbohydrates or lipids. Detection proceeds by any of a variety of knownmethods, including spectrophotometric or optical tracking of radioactiveor fluorescent markers, or other methods which track a molecule basedupon size, charge or affinity. A detectable moiety can be of anymaterial having a detectable physical or chemical property. Suchdetectable labels have been well-developed in the field of gelelectrophoresis, column chromatograpy, solid substrates, spectroscopictechniques, and the like, and in general, labels useful in such methodscan be applied to the present invention. Thus, a label is anycomposition detectable by spectroscopic, photochemical, biochemical,immunochemical, electrical, optical thermal, or chemical means. Usefullabels in the present invention include fluorescent dyes (e.g.,fluorescein isothiocyanate, Texas red, rhodamiine, and the like),radiolabels (e.g., 3H, 125I, 35S, 14C, 32P or 33P), enzymes (e.g., LacZ,chloramphenicol acetyltransferase (CAT), horse radish peroxidase,alkaline phosphatase and others, commonly used as detectable enzymes,either as marker products or as in an ELISA), nucleic acid intercalators(e.g., ethidium bromide) and colorimetric labels such as colloidal goldor colored glass or plastic (e.g. polystyrene, polypropylene, latex,etc.) beads.

Fluorescent labels are particularly preferred labels. Preferred labelsare typically characterized by one or more of the following: highsensitivity, high stability, low background, low environmentalsensitivity and high specificity in labeling.

Fluorescent moieties, which are incorporated into the labels of theinvention, are generally are known, including 1- and 2-aminonaphthalene,p,p′-diaminostilbenes, pyrenes, quaternary phenanthridine salts,9-aminoacridines, p,p′-diaminobenzophenone imines, anthracenes,oxacarbocyanine, merocyanine, 3-aminoequilenin, perylene,bis-benzoxazole, bis-p-oxazolyl benzene, 1,2-benzophenazin, retinol,bis-3-aminopyridinium salts, hellebrigenin, tetracycline, sterophenol,benzimidazolylphenylamine, 2-oxo-3-chromen, indole, xanthen,7-hydroxycoumarin, phenoxazine, calicylate, strophanthidin, porphyrins,triarylmethanes and flavin. Individual fluorescent compounds which havefunctionalities for linking to an element desirably detected in anapparatus or assay of the invention, or which can be modified toincorporate such functionalities include, e.g., dansyl chloride;fluoresceins such as 3,6-dihydroxy-9-phenylxanthhydrol;rhodamineisothiocyanate; N-phenyl 1-amino-8-sulfonatonaphthalene;N-phenyl 2-amino-6-sulfonatonaphthalene;4-acetamido-4-isothiocyanato-stilbene-2,2′-disulfonic acid;pyrene-3-sulfonic acid; 2-toluidinonaphthalene-6-sulfonate;N-phenyl-N-methyl-2-aminoaphthalene-6-sulfonate; ethidium bromide;stebrine; auromine-0,2-(9′-anthroyl)palmitate; dansylphosphatidylethanolamine; N,N′-dioctadecyl oxacarbocyanine: N,N′-dihexyloxacarbocyanine; merocyanine, 4-(3′pyrenyl)stearate;d-3-aminodesoxy-equilenin; 12-(9′-anthroyl)stearate; 2-methylanthracene;9-vinylanthracene; 2,2′(vinylene-p-phenylene)bisbenzoxazole;p-bis(2-(4-methyl-5-phenyl-oxazolyl))benzene;6-dimethylamino-1,2-benzophenazin; retinol; bis(3′-aminopyridinium)1,10-decandiyl diiodide; sulfonaphthylhydrazone of hellibrienin;chlorotetracycline;N-(7-dimethylamino-4-methyl-2-oxo-3-chromenyl)maleimide;N-(p-(2-benzimidazolyl)-phenyl)maleimide; N-(4-fluoranthyl)maleimide;bis(homovanillic acid); resazarin;4-chloro-7-nitro-2,1,3-benzooxadiazole; merocyanine 540; resorufin; rosebengal; and 2,4-diphenyl-3(2H)-furanone. Many fluorescent tags arecommercially available from SIGMA chemical company (Saint Louis, Mo.),Molecular Probes, R&D systems (Minneapolis, Minn.), Pharmacia LKBBiotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (PaloAlto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee,Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc.(Gaithersberg, Md.), Fluka Chemica-Biochemika Analytika (Fluka ChemieAG, Buchs, Switzerland), and Applied Biosystems (Foster City, Calif.) aswell as other commercial sources known to one of skill.

Desirably, fluorescent labels absorb light above about 300 nm,preferably about 350 nm, and more preferably above about 400 nm, usuallyemitting at wavelengths greater than about 10 nm higher than thewavelength of the light absorbed. It should be noted that the absorptionand emission characteristics of the bound label may differ from theunbound label. Therefore, when referring to the various wavelengthranges and characteristics of the labels, it is intended to indicate thelabels as employed and not the label which is unconjugated andcharacterized in an arbitrary solvent.

Fluorescent labels are one preferred class of detectable labels, in partbecause by irradiating a fluorescent label with light, one can obtain aplurality of emissions. Thus, a single label can provide for a pluralityof measurable events. Detectable signal may also be provided bychemiluminescent and bioluminescent sources. Chemiluminescent sourcesinclude a compound which becomes electronically excited by a chemicalreaction and may then emit light which serves as the detectible signalor donates energy to a fluorescent acceptor. A diverse number offamilies of compounds have been found to provide chemiluminescence undera variety or conditions. One family of compounds is2,3-dihydro-1,4-phthalazinedione. The most popular compound is luminol,which is a 5-amino compound. Other members of the family include the5-amino-6,7,8-trimethoxy- and the dimethylamino[ca]benz analog. Thesecompounds can be made to luminesce with alkaline hydrogen peroxide orcalcium hypochlorite and base. Another family of compounds is the2,4,5-triphenylimidazoles, with lophine as the common name for theparent product. Chemiluminescent analogs include para-dimethylamino and-methoxy substituents. Chemiluminescence may also be obtained withoxalates, usually oxalyl active esters, e.g., p-nitrophenyl and aperoxide, e.g., hydrogen peroxide, under basic conditions. Other usefulchemiluminescent compounds are also known and available, including—N-alkyl acridinum esters (basic H₂O₂) and dioxetanes. Alternatively,luciferins may be used in conjunction with luciferase or lucigenins toprovide bioluminescence.

The label is coupled directly or indirectly to a molecule to be detected(a product, substrate, enzyme, or the like) according to methods wellknown in the art. As indicated above, a wide variety of labels are used,with the choice of label depending on the sensitivity required, ease ofconjugation of the compound, stability requirements, availableinstrumentation, and disposal provisions. Non radioactive labels areoften attached by indirect means. Generally, a ligand molecule (e.g.,biotin) is covalently bound to a polymer. The ligand then binds to ananti-ligand (e.g., streptavidin) molecule which is either inherentlydetectable or covalently bound to a signal system, such as a detectableenzyme, a fluorescent compound, or a chemiluminescent compound. A numberof ligands and anti-ligands can be used. Where a ligand has a naturalanti-ligand, for example, biotin, thyroxine, and cortisol, it can beused in conjunction with labeled, anti-ligands. Alternatively, anyhaptenic or antigenic compound can be used in combination with anantibody. Labels can also be conjugated directly to signal generatingcompounds, e.g., by conjugation with an enzyme or fluorophore. Enzymesof interest as labels will primarily be hydrolases, particularlyphosphatases, esterases and glycosidases, or oxidoreductases,particularly peroxidases. Fluorescent compounds include fluorescein andits derivatives, rhodamine and its derivatives, dansyl, umbelliferone,etc. Chemiluminescent compounds include luciferin, and2,3-dihydrophthalazinediones, e.g., luminol. Means of detecting labelsare well known to those of skill in the art. Thus, for example, wherethe label is a radioactive label, means for detection include ascintillation counter or photographic film as in autoradiography. Wherethe label is a fluorescent label, it may be detected by exciting thefluorochrome with the appropriate wavelength of light and detecting theresulting fluorescence, e.g., by microscopy, visual inspection, viaphotographic film, by the use of electronic detectors such as digitalcameras, charge coupled devices (CCDs) or photomultipliers andphototubes, and the like. Fluorescent labels and detection techniques,particularly microscopy and spectroscopy are preferred. Similarly,enzymatic labels are detected by providing appropriate substrates forthe enzyme and detecting the resulting reaction product. Finally, simplecolorimetric labels are often detected simply by observing the colorassociated with the label. For example, conjugated gold often appearspink, while various conjugated beads appear the color of the bead.

In preferred aspects, the continuous system generates a constant signalwhich varies only when a test compound is introduced that affects thesystem. Specifically, as the system components flow along the channel,they will produce a relatively constant signal level at a detection zoneor window of the channel. Test compounds are periodically introducedinto the channel and mixed with the system components. Where those testcompounds have an effect on the system, it will cause a deviation fromthe constant signal level at the detection window. This deviation maythen be correlated to the particular test compound screened.

One embodiment of a device for use in a serial or continuous assaygeometry is shown in FIG. 1. As shown, the overall device 100 isfabricated in a planar substrate 102. Suitable substrate materials aregenerally selected based upon their compatibility with the conditionspresent in the particular operation to be performed by the device. Suchconditions can include extremes of pH, temperature, salt concentration,and application of electrical fields. Additionally, substrate materialsare also selected for their inertness to critical components of ananalysis or synthesis to be carried out by the device.

Examples of useful substrate materials include, e.g., glass, quartz andsilicon as well as polymeric substrates, e.g. plastics. In the case ofconductive or semi-conductive substrates, it will generally be desirableto include an insulating layer on the substrate. This is particularlyimportant where the device incorporates electrical elements, e.g.,electrical material and fluid direction systems, sensors and the like.In the case of polymeric substrates, the substrate materials areoptionally rigid, semi-rigid, or non-rigid, opaque, semi-opaque ortransparent, depending upon the use for which they are intended. Forexample, devices which include an optical or visual detection element,will generally be fabricated, at least in part, from transparentmaterials to allow, or at least, facilitate that detection.Alternatively, transparent windows of, e.g., glass or quartz, areoptionally incorporated into the device for these types detectionelements. Additionally, the polymeric materials may have linear orbranched backbones, and are optionally crosslinked or non-crosslinked.Examples of particularly preferred polymeric materials include, e.g.,polydimethylsiloxanes (PDMS), polyurethane, polyvinylchloride (PVC)polystyrene, polysulfone, polycarbonate and the like.

The device shown in FIG. 1 includes a series of channels 110, 112, andoptional reagent channel 114, fabricated into the surface of thesubstrate. At least one of these channels will typically have very smallcross sectional dimensions, e.g., in the range of from about 0.1 μm toabout 500 μm. Preferably the cross-sectional dimensions of the channelswill be in the range of from about 0.1 to about 200 μm and morepreferably in the range of from about 0.1 to about 100 μm. Inparticularly preferred aspects, each of the channels will have at leastone cross-sectional dimension in the range of from about 0.1 μm to about100 μm. Although generally shown as straight channels, it will beappreciated that in order to maximize the use of space on a substrate,serpentine, saw tooth or other channel geometries, to incorporateeffectively longer channels in shorter distances.

Manufacturing of these microscale elements into the surface of thesubstrates may generally be carried out by any number ofmicrofabrication techniques that are well known in the art. For example,lithographic techniques are optionally employed in fabricating, e.g.,glass, quartz or silicon substrates, using methods well known in thesemiconductor manufacturing industries such as photolithographicetching, plasma etching or wet chemical etching. Alternatively,micromachining methods such as laser drilling, micromilling and the likeare optionally employed. Similarly, for polymeric substrates, well knownmanufacturing techniques may also be used. These techniques includeinjection molding or stamp molding methods where large numbers ofsubstrates are optionally produced using, e.g., rolling stamps toproduce large sheets of microscale substrates or polymer microcastingtechniques where the substrate is polymerized within a micromachinedmold.

The devices will typically include an additional planar element whichoverlays the channeled substrate enclosing and fluidly sealing thevarious channels to form conduits. Attaching the planar cover element isachieved by a variety of means, including, e.g., thermal bonding,adhesives or, in the case of certain substrates, e.g., glass, orsemi-rigid and non-rigid polymeric substrates, a natural adhesionbetween the two components. The planar cover element may additionally beprovided with access ports and/or reservoirs for introducing the variousfluid elements needed for a particular screen.

The device shown in FIG. 1 also includes reservoirs 104, 106 and 108,disposed and fluidly connected at the ends of the channels 110 and 114.As shown, sample channel 112, is used to introduce the plurality ofdifferent test compounds into the device. As such, this channel willgenerally be fluidly connected to a source of large numbers of separatetest compounds that will be individually introduced into the samplechannel 112 and subsequently into channel 110.

The introduction of large numbers of individual, discrete volumes oftest compounds into the sample is carried out by a number of methods.For example, micropipettors are optionally used to introduce the testcompounds into the device. In preferred aspects, an electropipettor isused which is fluidly connected to sample channel 112. An example ofsuch an electropipettor is described in, e.g., U.S. Pat. No. 5,779,868,the disclosure of which is hereby incorporated herein by reference inits entirety for all purposes. Generally, this electropipettor utilizeselectroosmotic fluid direction as described herein, to alternatelysample a number of test compounds, or “subject materials,” and spacercompounds. The pipettor then delivers individual, physically isolatedsample or test compound volumes in subject material regions, in series,into the sample channel for subsequent manipulation within the device.Individual samples are typically separated by a spacer region of lowionic strength spacer fluid. These low ionic strength spacer regionshave higher voltage drop over their length than do the higher ionicstrength subject material or test compound regions, thereby driving theelectrokinetic pumping. On either side of the test compound or subjectmaterial region, which is typically in higher ionic strength solution,are fluid regions referred to as first spacer regions (also referred toas “guard bands”), that contact the interface of the subject materialregions. These first spacer regions typically comprise a high ionicstrength solution to prevent migration of the sample elements into thelower ionic strength fluid regions, or second spacer region, which wouldresult in electrophoretic bias. The use of such first and second spacerregions is described in greater detail in U.S. Pat. No. 5,779,868 whichis incorporated herein by reference.

Alternatively, the sample channel 112 is optionally individually fluidlyconnected to a plurality of separate reservoirs via separate channels.The separate reservoirs each contain a separate test compound withadditional reservoirs being provided for appropriate spacer compounds.The test compounds and/or spacer compounds are then transported from thevarious reservoirs into the sample channels using appropriate materialdirection schemes. In either case, it generally is desirable to separatethe discrete sample volumes, or test compounds, with appropriate spacerregions.

As shown, the device also includes a detection window or zone 116 atwhich a signal from the biochemical system is optionally monitored. Thisdetection window typically will include a transparent cover allowingvisual or optical observation and detection of the assay results, e.g.,observation of a colorometric or fluorometric response.

In particularly preferred aspects, monitoring of the signals at thedetection window is achieved using an optical detection system. Forexample, fluorescence based signals are typically monitored using, e.g.,laser activated fluorescence detection systems which employ a laserlight source at an appropriate wavelength for activating the fluorescentindicator within the system. Fluorescence is then detected using anappropriate detector element, e.g., a photomultiplier tube (PMT).Similarly, for screens employing colorometric signals,spectrophotometric detection systems which direct a light source at thesample are optionally used, providing a measurement of absorbance ortransmissivity of the sample.

In alternative aspects, the detection system may comprise non-opticaldetectors or sensors for detecting a particular characteristic of thesystem disposed within detection window 116. Such sensors may includetemperature, conductivity, potentiometric (pH, ions), amperometric (forcompounds that are oxidized or reduced, e.g., O₂, H₂O₂, I₂,oxidizable/reducible organic compounds, and the like).

In operation, a flowable first component of a biological system, e.g., afluid comprising a receptor or enzyme, is placed in reservoir 104. Thisfirst component is flowed through main channel 110, past the detectionwindow, 116, and toward waste reservoir 108. A second component of thebiochemical system, e.g., a ligand or substrate, is concurrently flowedinto the main channel 110 from the side channel 114, whereupon the firstand second components mix and are able to interact. Deposition of theseelements within the device is carried out in a number of ways. Forexample, the enzyme and substrate, or receptor and ligand solutions canbe introduced into the device through open or sealable access ports inthe planar cover. Alternatively, these components are optionally addedto their respective reservoirs during manufacture of the device. In thecase of such pre-added components, it is desirable to provide thesecomponents in a stabilized form to allow for prolonged shelf-life of thedevice. For example, the enzyme/substrate or receptor/ligand componentsare optionally provided within the device in lyophilized form. Prior touse, these components are easily reconstituted by introducing a buffersolution into the reservoirs. Alternatively, the components arelyophilized with appropriate buffering salts, whereby simple wateraddition is all that is required for reconstitution.

As noted above, the interaction of the first and second components istypically accompanied by a detectable signal. For example, in thoseembodiments where the first component is an enzyme and the second asubstrate, the substrate is a chromogenic or fluorogenic substrate whichproduces an optically detectable signal when the enzyme acts upon thesubstrate. In the case where the first component is a receptor and thesecond is a ligand, either the ligand or the receptor optionallyincludes a detectable signal. In either event, the mixture and flow rateof compounds will typically remain constant such that the flow of themixture of the first and second components past the detection window 116will produce a steady-state signal. By “steady state signal” isgenerally meant a signal that has a regular, predictable signalintensity profile. As such, the steady-state signal may include signalshaving a constant signal intensity, or alternatively, a signal with aregular periodic intensity, against which variations in the normalsignal profile is measured. This latter signal is generated in caseswhere fluid flow is periodically interrupted for, e.g., loadingadditional test compounds, as described in the description of thecontinuous flow systems. Although the signal produced in theabove-described enzymatic system will vary along the length of thechannel, i.e., increasing with time of exposure as the enzyme convertsthe fluorogenic substrate to the fluorescent product, the signal at anyspecific point along the channel will remain constant, given a constantflow rate.

From sample channel 112, test compounds is periodically or seriallyintroduced into the main channel 110 and into the stream of first andsecond components as fluid regions containing the test compound, alsoreferred to as the “subject material regions.” Where these testcompounds have an effect on the interaction of the first and secondelements, it will produce a deviation in the signal detected at thedetection window corresponding to the subject material region. As notedabove, typically, the various different test compounds to be injectedthrough channel 112 will be separated by a first and even second spacerfluid regions to allow differentiation of the effects, or lack ofeffects, from one test compound to another. In those embodiments whereelectroosmotic fluid direction systems are employed, the spacer fluidregions may also function to reduce any electrophoretic bias that canoccur within the test sample. The use of these spacer regions to drivethe electroosmotic flow of fluids, as well as in the general eliminationof electrophoretic bias within the sample or test compound or subjectmaterial regions is substantially described in U.S. Pat. No. 5,779,868,previously incorporated herein by reference.

By way of example, a steady, continuous flow of enzyme and fluorogenicsubstrate through main channel 110 will produce a constant fluorescentsignal at the detection window 116. Where a test compound inhibits theenzyme, introduction of a test compound, i.e., in a subject materialregion, will produce a momentary but detectable drop in the level ofsignal at the detection window corresponding with that subject materialregion. The timing of the drop in signal can then be correlated with aparticular test compound based upon a known injection to detectiontime-frame. Specifically, the time required for an injected compound toproduce an observed effect can be readily determined using positivecontrols.

For receptor/ligand systems, a similar variation in the steady statesignal may also be observed. Specifically, the receptor and itsfluorescent ligand can be made to have different flow rates along thechannel. This can be accomplished by incorporating size exclusionmatrices within the channel, or, in the case of electroosmotic methods,altering the relative electrophoretic mobility of the two compounds sothat the receptor flows more rapidly down the channel. Again, this isaccomplished through the use of size exclusion matrices, or through theuse of different surface charges in the channel which will result indifferential flow rates of charge-varied compounds. Where a testcompound binds to the receptor, it will result in a dark pulse in thefluorescent signal followed by a brighter pulse. Without being bound toa particular theory of operation, it is believed that the steady statesignal is a result of both free fluorescent ligand, and fluorescentligand bound to the receptor. The bound ligand is traveling at the sameflow rate as the receptor while the unbound ligand is traveling moreslowly. Where the test compound inhibits the receptor-ligandinteraction, the receptor will not ‘bring along’ the fluorescent ligand,thereby diluting the fluorescent ligand in the direction of flow, andleaving an excess of free fluorescent ligand behind. This results in atemporary reduction in the steady-state signal, followed by a temporaryincrease in fluorescence. Alternatively, schemes similar to thoseemployed for the enzymatic system is employed, where there is a signalthat reflects the interaction of the receptor with its ligand. Forexample, pH indicators which indicate pH effects of receptor-ligandbinding is incorporated into the device along with the biochemicalsystem, i.e., in the form of encapsulated cells, whereby slight pHchanges resulting from binding can be detected. See Weaver, et al.,Bio/Technology (1988) 6:1084–1089. Additionally, one can monitoractivation of enzymes resulting from receptor ligand binding, e.g.,activation of kinases, or detect conformational changes in such enzymesupon activation, e.g., through incorporation of a fluorophore which isactivated or quenched by the conformational change to the enzyme uponactivation.

Flowing and direction of fluids within the microscale fluidic devices iscarried out by a variety of methods. For example, the devices mayinclude integrated microfluidic structures, such as micropumps andmicrovalves, or external elements, e.g., pumps and switching valves, forthe pumping and direction of the various fluids through the device.Examples of microfluidic structures are described in, e.g., U.S. Pat.Nos. 5,271,724, 5,277,556, 5,171,132, and 5,375,979. See also, PublishedU.K. Patent Application No. 2 248 891 and Published European PatentApplication No. 568 902.

Although microfabricated fluid pumping and valving systems are readilyemployed in the devices of the invention, the cost and complexityassociated with their manufacture and operation can generally prohibittheir use in mass-produced disposable devices as are envisioned by thepresent invention. For that reason, in particularly preferred aspects,the devices of the invention will typically include an electroosmoticfluid direction system. Such fluid direction systems combine theelegance of a fluid direction system devoid of moving parts, with anease of manufacturing, fluid control and disposability. Examples ofparticularly preferred electroosmotic fluid direction systems include,e.g., those described in International Patent Application No. WO96/04547 to Ramsey et al., which is incorporated herein by reference inits entirety for all purposes.

In brief, these fluidic control systems typically include electrodesdisposed within the reservoirs that are placed in fluid connection withthe plurality of intersecting channels fabricated into the surface ofthe substrate. The materials stored in the reservoirs are transportedthrough the channel system delivering appropriate volumes of the variousmaterials to one or more regions on the substrate in order to carry outa desired screening assay.

Fluid and materials transport and direction is accomplished throughelectroosmosis or electrokinesis. In brief, when an appropriatematerial, typically comprising a fluid, is placed in a channel or otherfluid conduit having functional groups present at the surface, thosegroups can ionize. For example, where the surface of the channelincludes hydroxyl functional groups at the surface, protons can leavethe surface of the channel and enter the fluid. Under such conditions,the surface will possess a net negative charge, whereas the fluid willpossess an excess of protons or positive charge, particularly localizednear the interface between the channel surface and the fluid. Byapplying an electric field along the length of the channel, cations willflow toward the negative electrode. Movement of the positively chargedspecies in the fluid pulls the solvent with them. The steady statevelocity of this fluid movement is generally given by the equation:

$v = \frac{\varepsilon\mspace{11mu}\xi\; E}{4\;\pi\;\eta}$where v is the solvent velocity, ε is the dielectric constant of thefluid, ξ is the zeta potential of the surface, E is the electric fieldstrength, and η is the solvent viscosity. Thus, as can be easily seenfrom this equation, the solvent velocity is directly proportional to thesurface potential.

To provide appropriate electric fields, the system generally includes avoltage controller that is capable of applying selectable voltagelevels, simultaneously, to each of the reservoirs, including ground.Such a voltage controller can be implemented using multiple voltagedividers and multiple relays to obtain the selectable voltage levels.Alternatively, multiple, independent voltage sources are optionallyused. The voltage controller is electrically connected to each of thereservoirs via an electrode positioned or fabricated within each of theplurality of reservoirs.

Incorporating this electroosmotic fluid direction system into the deviceshown in FIG. 1 involves incorporation of an electrode within each ofthe reservoirs 104, 106 and 108, and at the terminus of sample channel112 or at the terminus of any fluid channels connected thereto, wherebythe electrode is in electrical contact with the fluid disposed in therespective reservoir or channel. Substrate materials are also selectedto produce channels having a desired surface charge. In the case ofglass substrates, the etched channels will possess a net negative chargeresulting from the ionized hydroxyls naturally present at the surface.Alternatively, surface modifications are optionally employed to providean appropriate surface charge, e.g., coatings, derivatization, e.g.,silanation, or impregnation of the surface to provide appropriatelycharged groups on the surface. Examples of such treatments are describedin, e.g., Provisional Patent Application Ser. No. 60/015,498, filed Apr.16, 1996 (Abandoned) which is hereby incorporated herein by reference inits entirety for all purposes.

In brief, suitable substrate materials are generally selected based upontheir compatibility with the conditions present in the particularoperation to be performed by the device. Such conditions can includeextremes of pH, temperature and salt concentration. Additionally,substrate materials are also selected for their inertness to criticalcomponents of an analysis or synthesis to be carried out by the device.Polymeric substrate materials may be rigid, semi-rigid, or non-rigid,opaque, semi-opaque or transparent, depending upon the use for whichthey are intended. For example, devices which include an optical orvisual detection element, will generally be fabricated, at least inpart, from a transparent polymeric material to facilitate thatdetection. Alternatively, transparent windows of, e.g. glass or quartz,may be incorporated into the device for these detection elements.Additionally, the polymeric materials may have linear or branchedbackbones, and may be crosslinked or non-crosslinked. Examples ofpolymeric materials include, e.g., Acrylics, especially PMMAs(polymethylmethacrylates); exemplar acrylics include e.g., Acrylite M-30or Acrylite L-40 available from CYRO Industries, Rockaway, N.J., orPLEXIGLAS VS UVT available from Autohaas North America; polycarbonates(e.g., Makrolon CD-2005 available from The Plastics and Rubber divisionof Mobay Corporation (Pittsburg, Pa.) or Bayer Corporation, or LEXAN OQ1020L or LEXAN OQ 1020, both available from GE Plastics)polydimethylsiloxanes (PDMS), polyurethane, polyvinylchloride (PVC)polystyrene, polysulfone, polycarbonate and the like. Optical,mechanical, thermal, electrical, and chemical resistance properties formany plastics are well known (and are generally available from themanufacturer), or can easily be determined by standard assays.

As described herein, the electrokinetic fluid control systems employedin the devices of the present invention generally utilize a substratehaving charged functional groups at its surface, such as the hydroxylgroups present on glass surfaces. As described, devices of the presentinvention can also employ plastic or other polymeric substrates. Ingeneral, these substrate materials have hydrophobic surfaces. As aresult, use of electrokinetic fluid control systems in devices utilizingpolymeric substrates used in the present invention typically employsmodification of the surfaces of the substrate that are in contact withfluids.

Surface modification of polymeric substrates may take on a variety ofdifferent forms. For example, surfaces may be coated with anappropriately charged material. For example, surfactants with chargedgroups and hydrophobic tails are desirable coating materials. In short,the hydrophobic tails will localize to the hydrophobic surface of thesubstrate, thereby presenting the charged head group at the fluid layer.

In one embodiment, preparation of a charged surface on the substrateinvolves the exposure of the surface to be modified, e.g., the channelsand/or reaction chambers, to an appropriate solvent which partiallydissolves or softens the surface of the polymeric substrate. A detergentis then contacted with the partially dissolved surface. The hydrophobicportion of the detergent molecules will associate with the partiallydissolve polymer. The solvent is then washed from the surface, e.g.,using water, whereupon the polymer surface hardens with the detergentembedded into the surface, presenting the charged head group to thefluid interface.

In alternative aspects, polymeric materials, such aspolydimethylsiloxane, may be modified by plasma irradiation. Inparticular, plasma irradiation of PDMS oxidizes the methyl groups,liberating the carbons and leaving hydroxyl groups in their place,effectively creating a glass-like surface on the polymeric material,with its associated hydroxyl functional groups.

The polymeric substrate may be rigid, semi-rigid, nonrigid or acombination of rigid and nonrigid elements, depending upon theparticular application for which the device is to be used. In oneembodiment, a substrate is made up of at least one softer, flexiblesubstrate element and at least one harder, more rigid substrate element,one of which includes the channels and chambers manufactured into itssurface. Upon mating the two substrates, the inclusion of the softelement allows formation of an effective fluid seal for the channels andchambers, obviating the need and problems associated with gluing ormelting more rigid plastic components together.

A number of additional elements are added to the polymeric substrate toprovide for the electrokinetic fluid control systems. These elements maybe added either during the substrate formation process, i.e., during themolding or stamping steps, or they may be added during a separate,subsequent step. These elements typically include electrodes for theapplication of voltages to the various fluid reservoirs, and in someembodiments, voltage sensors at the various channel intersections tomonitor the voltage applied.

Electrodes may be incorporated as a portion of the molding process. Inparticular, the electrodes may be patterned within the mold so that uponintroduction of the polymeric material into the mold, the electrodeswill be appropriately placed. Alternatively, the electrodes and otherelements may be added after the substrate is formed, using well knownmicrofabrication methods, e.g., sputtering or controlled vapordeposition methods followed by chemical etching.

Whether polymeric or other substrates are used, modulating voltages areconcomitantly applied to the various reservoirs to affect a desiredfluid flow characteristic, e.g., continuous flow of receptor/enzyme,ligand/substrate toward the waste reservoir with the periodicintroduction of test compounds. Particularly, modulation of the voltagesapplied at the various reservoirs can move and direct fluid flow throughthe interconnected channel structure of the device in a controlledmanner to effect the fluid flow for the desired screening assay andapparatus.

FIG. 2A shows a schematic illustration of fluid direction during atypical assay screen. Specifically, shown is the injection of a testcompound (in a subject material region) into a continuous stream of anenzyme-fluorogenic substrate mixture. As shown in FIG. 2A, and withreference to FIG. 1, a continuous stream of enzyme is flowed fromreservoir 104, along main channel 110. Test compounds 120, separated byappropriate spacer regions 121, e.g., low ionic strength spacer regions,are introduced from sample channel 112 into main channel 110. Onceintroduced into the main channel, the test compounds will interact withthe flowing enzyme stream. The mixed enzyme/test compound regions arethen flowed along main channel 110 past the intersection with channel114. A continuous stream of fluorogenic or chromogenic substrate whichis contained in reservoir 106, is introduced into sample channel 110,whereupon it contacts and mixes with the continuous stream of enzyme,including the subject material regions which include the test compounds122. Action of the enzyme upon the substrate will produce an increasinglevel of the fluorescent or chromatic signal. This increasing signal isindicated by the increasing shading within the main channel as itapproaches the detection window. This signal trend will also occurwithin those test compound or subject material regions which have noeffect on the enzyme/substrate interaction, e.g., test compound 126.Where a test compound does have an effect on the interaction of theenzyme and the substrate, a variation will appear in the signalproduced. For example, assuming a fluorogenic substrate, a test compoundwhich inhibits the interaction of the enzyme with its substrate willresult in less fluorescent product being produced within that subjectmaterial region. This will result in a non-fluorescent, or detectablyless fluorescent region within the flowing stream as it passes detectionwindow 116, which corresponds to the subject material region. Forexample, as shown, a subject material region including a test compound128, which is a putative inhibitor of the enzyme-substrate interaction,shows detectably lower fluorescence than the surrounding stream. This isindicated by a lack of shading of subject material region 128.

A detector adjacent to the detection window monitors the level offluorescent signal being produced by the enzyme's activity on thefluorogenic or chromogenic substrate. This signal remains at arelatively constant level for those test compounds which have no effecton the enzyme-substrate interaction. When an inhibitory compound isscreened, however, it will produce a momentary drop in the fluorescentsignal representing the reduced or inhibited enzyme activity toward thesubstrate. Conversely, inducer compounds, upon screening, produce amomentary increase in the fluorescent signal, corresponding to theincreased enzyme activity toward the substrate.

FIG. 2B provides a similar schematic illustration of a screen foreffectors of a receptor-ligand interaction. As in FIG. 2A, a continuousstream of receptor is flowed from reservoir 104 through main channel110. Test compounds or subject material regions 150 separated byappropriate spacer fluid regions 121 are introduced into the mainchannel 110 from sample channel 112, and a continuous stream offluorescent ligand from reservoir 106 is introduced from side channel114. Fluorescence is indicated by shading within the channel. As in FIG.2A, the continuous stream of fluorescent ligand and receptor past thedetection window 116 will provide a constant signal intensity. Thesubject material regions in the stream, containing the test compoundswhich have no effect on the receptor-ligand interaction, will providethe same or similar level of fluorescence as the rest of the surroundingstream, e.g., test compound or subject material region 152. However, thepresence of test compounds which possess antagonistic or inhibitoryactivity toward the receptor-ligand interaction will result in lowerlevels of that interaction in those portions of the stream where thosecompounds are located, e.g., test compound or subject material region154. Further, differential flow rates for the receptor bound fluorescentligand and free fluorescent ligand will result in a detectable drop inthe level of fluorescence which corresponds to the dilution of thefluorescence resulting from unbound, faster moving receptor. The drop influorescence is then followed by an increase in fluorescence 156 whichcorresponds to an accumulation of the slower moving, unbound fluorescentligand.

In some embodiments, it is desirable to provide an additional channelfor shunting off or extracting the subject material region reactionmixture from the running buffer and/or spacer regions. This may be thecase where one wishes to keep the reaction elements contained within thea discrete fluid region during the reaction, while allowing theseelements to be separated during a data acquisition stage. As describedpreviously, one can keep the various elements of the reaction togetherin the subject material region that is moving through the reactionchannel by incorporating appropriate spacer fluid regions betweensamples. Such spacer fluid regions are generally selected to retain thesamples within their original subject material regions, i.e., notallowing smearing of the sample into the spacer regions, even duringprolonged reaction periods. However, this goal can be at odds with thoseassays which are based upon the separation of elements of the assay,e.g., ligand-receptor assays described above, or where a reactionproduct must be separated in a capillary. Thus, it may be desirable toremove those elements which prevented such separation during the initialportions of the fluid direction.

A schematic illustration of one embodiment of a device 500 forperforming this sample or subject material shunting or extraction isshown in FIG. 5. As shown, the subject materials or test compounds 504are introduced to the device or chip via the sample channel 512. Again,these are typically introduced via an appropriate injection device 506,e.g., a capillary pipettor. The ionic strength and lengths of the firstspacer regions 508 and second spacer regions 502 are selected such thatthose samples with the highest electrophoretic mobility will not migratethrough the first spacer regions 508 into the second spacer regions 502in the length of time that it takes the sample to travel down thereaction channel.

Assuming a receptor ligand assay system, test compounds pass into thedevice 500 and into reaction channel 510, where they are first combinedwith the receptor. The test compound/receptor, in the form of thesubject material regions, are flowed along the reaction channel in theincubation zone 510 a. Following this initial incubation, the testcompound/receptor mix is combined with a labelled ligand (e.g.,fluorescent ligand) whereupon this mixture flows along the secondincubation region 510 b of reaction channel 510. The lengths of theincubation regions and the flow rates of the system (determined by thepotentials applied at each of the reservoirs 514, 516, 518, 520, 522,and at the terminus of sample channel 512) determine the time ofincubation of the receptor with the fluorescent ligand and testcompound. The ionic strengths of the solutions containing the receptorsand fluorescent ligands, as well as the flow rates of material from thereservoirs housing these elements into the sample channel are selectedso as to not interfere with the first and second spacer regions.

The isolated subject material regions containing receptor, fluorescentligand and test compound are flowed along the reaction channel 510 bythe application of potentials at, e.g., reservoirs 514, 516, 518 and atthe terminus of sample channel 512. Potentials are also applied atreservoirs 520 and 522, at the opposite ends of separation channel 524,to match the potentials at the two ends of the transfer channel, so thatthe net flow across the transfer channel is zero. As the subjectmaterial region passes the intersection of reaction channel 510 andtransfer channel 526, the potentials are allowed to float at reservoirs518 and 522, whereupon the potentials applied at reservoirs 514, 516,520, and at the terminus of sample channel 512, result in the subjectmaterial region being shunted through transfer channel 526 and intoseparation channel 524. Once in the separation channel, the originalpotentials are reapplied to all of the reservoirs to stop the net fluidflow through transfer channel 526. The diversion of the subject materialcan then be repeated with each subsequent subject material region.Within the separation channel, the subject material region is exposed todifferent conditions than those of the reaction channel. For example, adifferent flow rate may be used, capillary treatments may allow forseparation of differentially charged or different sized species, and thelike. In a preferred aspect, the subject material is shunted into theseparation channel to place the subject material into a capillary filledwith high ionic strength buffer, i.e., to remove the low ionic strengthspacer regions, thereby allowing separation of the various samplecomponents outside the confines of the original subject material region.For example, in the case of the above-described receptor/ligand screen,the receptor/ligand complex may have a different electrophoreticmobility from the ligand alone, in the transfer channel, therebyallowing more pronounced separation of the complex from the ligand, andits subsequent detection.

Such modifications have a wide variety of uses, particularly where it isdesirable to separate reaction products following reaction, e.g., incleavage reactions, fragmentation reactions, PCR reactions, and thelike.

C. Serial in Parallel Assay Systems

More complex systems can also be produced within the scope of thepresent invention. For example, a schematic illustration of onealternate embodiment employing a “serial input parallel reaction”geometry is shown in FIG. 3. As shown, the device 300 again includes aplanar substrate 302 as described previously. Fabricated into thesurface of the substrate 302 are a series of parallel reaction channels312–324. Also shown are three transverse channels fluidly connected toeach of these parallel reaction channels. The three transverse channelsinclude a sample injection channel 304, an optional seeding channel 306and a collection channel 308. Again, the substrate and channels aregenerally fabricated utilizing the materials and to the dimensionsgenerally described above. Although shown and described in terms of aseries of parallel channels, the reaction channels may also befabricated in a variety of different orientations. For example, ratherthan providing a series of parallel channels fluidly connected to asingle transverse channel, the channels are optionally fabricatedconnecting to and extending radially outward from a central reservoir,or are optionally arranged in some other non-parallel fashion.Additionally, although shown with three transverse channels, it will berecognized that fewer transverse channels are used where, e.g., thebiochemical system components are predisposed within the device.Similarly, where desired, more transverse channels are optionally usedto introduce further elements into a given assay screen. Accordingly,the serial-in-parallel devices of the present invention will typicallyinclude at least two and preferably three, four, five or more transversechannels. Similarly, although shown with 7 reaction channels, it will bereadily appreciated that the microscale devices of the present inventionwill be capable of comprising more than 7 channels, depending upon theneeds of the particular screen. In preferred aspects, the devices willinclude from 10 to about 500 reaction channels, and more preferably,from 20 to about 200 reaction channels.

This device may be particularly useful for screening test compoundsserially injected into the device, but employing a parallel assaygeometry, once the samples are introduced into the device, to allow forincreased throughput.

In operation, test compounds in discrete subject material regions, areserially introduced into the device, separated as described above, andflowed along the transverse sample injection channel 304 until theseparate subject material regions are adjacent the intersection of thesample channel 304 with the parallel reaction channels 310–324. As shownin FIGS. 4A–4F, the test compounds are optionally provided immobilizedon individual beads. In those cases where the test compounds areimmobilized on beads, the parallel channels are optionally fabricated toinclude bead resting wells 326–338 at the intersection of the reactionchannels with the sample injection channel 304. Arrows 340 indicate thenet fluid flow during this type of sample/bead injection. As individualbeads settle into a resting well, fluid flow through that particularchannel will be generally restricted. The next bead in the seriesfollowing the unrestricted fluid flow, then flows to the next availableresting well to settle in place.

Once in position adjacent to the intersection of the parallel reactionchannel and the sample injection channel, the test compound is directedinto its respective reaction channel by redirecting fluid flows downthose channels. Again, in those instances where the test compound isimmobilized on a bead, the immobilization will typically be via acleavable linker group, e.g., a photolabile, acid or base labile linkergroup. Accordingly, the test compound will typically need to be releasedfrom the bead, e.g., by exposure to a releasing agent such as light,acid, base or the like prior to flowing the test compound down thereaction channel.

Within the parallel channel, the test compound will be contacted withthe biochemical system for which an effector compound is being sought.As shown, the first component of the biochemical system is placed intothe reaction channels using a similar technique to that described forthe test compounds. In particular, the biochemical system is typicallyintroduced via one or more transverse seeding channels 306. Arrows 342illustrate the direction of fluid flow within the seeding channel 306.The biochemical system are optionally solution based, e.g., acontinuously flowing enzyme/substrate or receptor-ligand mixture, likethat described above, or as shown in FIGS. 4A–4F, may be a whole cell orbead based system, e.g., beads which have enzyme/substrate systemsimmobilized thereon.

In those instances where the biochemical system is incorporated in aparticle, e.g., a cell or bead, the parallel channel may include aparticle retention zone 344. Typically, such retention zones willinclude a particle sieving or filtration matrix, e.g., a porous gel ormicrostructure which retains particulate material but allows the freeflow of fluids. Examples of microstructures for this filtration include,e.g., those described in U.S. Pat. No. 5,304,487, which is herebyincorporated by reference in its entirety for all purposes. As with thecontinuous system, fluid direction within the more complex systems maybe generally controlled using microfabricated fluid directionstructures, e.g., pumps and valves. However, as the systems grow morecomplex, such systems become largely unmanageable. Accordingly,electroosmotic systems, as described above, are generally preferred forcontrolling fluid in these more complex systems. Typically, such systemswill incorporate electrodes within reservoirs disposed at the termini ofthe various transverse channels to control fluid flow thorough thedevice. In some aspects, it is desirable to include electrodes at thetermini of all the various channels. This generally provides for moredirect control, but also grows less manageable as systems grow morecomplex. In order to utilize fewer electrodes and thus reduce thepotential complexity, it may often be desirable in parallel systems,e.g., where two fluids are desired to move at similar rates in parallelchannels, to adjust the geometries of the various flow channels. Inparticular, as channel length increases, resistance along that channelwill also increase. As such, flow lengths between electrodes should bedesigned to be substantially the same regardless of the parallel pathchosen. This will generally prevent the generation of transverseelectrical fields and thus promote equal flow in all parallel channels.To accomplish substantially the same resistance between the electrodes,one can alter the geometry of the channel structure to provide for thesame channel length, and thus, the channel resistance, regardless of thepath travelled. Alternatively, resistance of channels are optionallyadjusted by varying the cross-sectional dimensions of the paths, therebycreating uniform resistance levels regardless of the path taken.

As the test compounds are drawn through their respective parallelreaction channels, they will contact the biochemical system in question.As described above, the particular biochemical system will typicallyinclude a flowable indicator system which indicates the relativefunctioning of that system, e.g., a soluble indicator such aschromogenic or fluorogenic substrate, labelled ligand, or the like, or aparticle based signal, such as a precipitate or bead bound signallinggroup. The flowable indicator is then flowed through the respectiveparallel channel and into the collection channel 308 whereupon thesignals from each of the parallel channels are flowed, in series, pastthe detection window, 116.

FIGS. 4A–4F, with reference to FIG. 3, show a schematic illustration ofthe progression of the injection of test compounds and biochemicalsystem components into the “serial input parallel reaction” device,exposure of the system to the test compounds, and flowing of theresulting signal out of the parallel reaction channels and past thedetection window. In particular, FIG. 4A shows the introduction of testcompounds immobilized on beads 346 through sample injection channel 304.Similarly, the biochemical system components 348 are introduced into thereaction channels 312–324 through seeding channel 306. Although shown asbeing introduced into the device along with the test compounds, asdescribed above, the components of the model system to be screened areoptionally incorporated into the reaction channels during manufacture.Again, such components are optionally provided in liquid form or inlyophilized form for increased shelf life of the particular screeningdevice.

As shown, the biochemical system components are embodied in a cellularor particle based system, however, fluid components may also be used asdescribed herein. As the particulate components flow into the reactionchannels, they are optionally retained upon an optional particleretaining matrix 344, as described above.

FIG. 4B illustrates the release of test compounds from the beads 346 byexposing the beads to a releasing agent. As shown, the beads are exposedto light from an appropriate light source 352, e.g., which is able toproduce light in a wavelength sufficient to photolyze the linker group,thereby releasing compounds that are coupled to their respective beadsvia a photolabile linker group.

In FIG. 4C, the released test compounds are flowed into and along theparallel reaction channels as shown by arrows 354 until they contact thebiochemical system components. The biochemical system components 348 arethen allowed to perform their function, e.g., enzymatic reaction,receptor/ligand interaction, and the like, in the presence of the testcompounds. Where the various components of the biochemical system areimmobilized on a solid support, release of the components from theirsupports can provide the initiating event for the system. A solublesignal 356 which corresponds to the functioning of the biochemicalsystem is then generated (FIG. 4D). As described previously, a variationin the level of signal produced is an indication that the particulartest compound is an effector of the particular biochemical system. Thisis illustrated by the lighter shading of signal 358.

In FIGS. 4E and 4F, the soluble signal is then flowed out of reactionschannels 312–324 into the detection channel 308, and along the detectionchannel past the detection window 116.

Again, a detection system as described above, located adjacent thedetection window will monitor the signal levels. In some embodiments,the beads which bore the test compounds are optionally recovered toidentify the test compounds which were present thereon. This istypically accomplished by incorporation of a tagging group during thesynthesis of the test compound on the bead. As shown, spent bead 360,i.e., from which a test compound has been released, is optionallytransported out of the channel structure through port 362 foridentification of the test compound that had been coupled to it. Suchidentification are optionally accomplished outside of the device bydirecting the bead to a fraction collector, whereupon the test compoundspresent on the beads are optionally identified, either throughidentification of a tagging group, or through identification of residualcompounds. Incorporation of tagging groups in combinatorial chemistrymethods has been previously described using encrypted nucleotidesequences or chlorinated/fluorinated aromatic compounds as tagginggroups. See, e.g., Published PCT Application No. WO 95/12608.Alternatively, the beads are optionally transported to a separate assaysystem within the device itself whereupon the identification is carriedout.

FIG. 6A shows an alternate embodiment of a “serial input parallelreaction” device which can be used for fluid based as opposed to beadbased systems. As shown the device 600 generally incorporates at leasttwo transverse channels as were shown in FIGS. 3 and 4, namely, sampleinjection channel 604 and detection channel 606. These transversechannels are interconnected by the series of parallel channels 612–620which connect sample channel 604 to detection channel 606.

The device shown also includes an additional set of channels fordirecting the flow of fluid test compounds into the reaction channels.In particular, an additional transverse pumping channel 634 is fluidlyconnected to sample channel 604 via a series of parallel pumpingchannels 636–646. The pumping channel includes reservoirs 650 and 652 atits termini. The intersections of parallel channels 636–646 arestaggered from the intersections of parallel channels 612–620 withsample channel 604, e.g., half way between. Similarly, transversepumping channel 608 is connected to detection channel 606 via parallelpumping channels 622–632. Again, the intersections of parallel pumpingchannels 622–632 with detection channel 606 are staggered from theintersections of reaction channels 612–620 with the detection channel606.

A schematic illustration of the operation of this system is shown inFIGS. 6B–6C. As shown, a series of test compounds, physically isolatedfrom each other in separate subject material regions, are introducedinto sample channel 604 using the methods described previously. Forelectroosmotic systems, potentials are applied at the terminus of samplechannel 604, as well as reservoir 648. Potentials are also applied atreservoirs 650:652, 654:656, and 658:660. This results in a fluid flowalong the transverse channels 634, 604, 606 and 608, as illustrated bythe arrows, and a zero net flow through the parallel channel arraysinterconnecting these transverse channels, as shown in FIG. 6B. Once thesubject material regions containing the test compounds are aligned withparallel reaction channels 612–620, connecting sample channel 604 todetection channel 606, as shown by the shaded areas in FIG. 6B, flow isstopped in all transverse directions by removing the potentials appliedto the reservoirs at the ends of these channels. As described above, thegeometry of the channels can be varied to maximize the use of space onthe substrate. For example, where the sample channel is straight, thedistance between reaction channels (and thus, the number of parallelreactions that can be carried out in a size limited substrate) isdictated by the distance between subject material regions. Theserestrictions, however, can be eliminated through the inclusion ofaltered channel geometries. For example, in some aspects, the length ofa first and second spacer regions can be accommodated by a serpentine,square-wave, saw tooth or other reciprocating channel geometry. Thisallows packing a maximum number of reaction channels onto the limitedarea of the substrate surface.

Once aligned with the parallel reaction channels, the sample, or subjectmaterial, is then moved into the parallel reaction channels 612–620 byapplying a first potential to reservoirs 650 and 652, while applying asecond potential to reservoirs 658 and 660, whereby fluid flow throughparallel pumping channels 636–646 forces the subject material intoparallel reaction channels 612–620, as shown in FIG. 6C. During thisprocess, no potential is applied at reservoirs—648, 654, 656, or theterminus of sample channel 604. Parallel channels 636–646 and 622–632are generally adjusted in length such that the total channel length, andthus the level of resistance, from reservoirs 650 and 652 to channel 604and from reservoirs 658 and 660 to channel 606, for any path taken willbe the same. Resistance can generally be adjusted by adjusting channellength or width. For example, channels can be lengthened by includingfolding or serpentine geometries. Although not shown as such, toaccomplish this same channel length, channels 636 and 646 would be thelongest and 640 and 642 the shortest, to create symmetric flow, therebyforcing the samples into the channels. As can be seen, during flowing ofthe samples through channels 612–620, the resistance within thesechannels will be the same, as the individual channel length is the same.

Following the reaction to be screened, the subject materialregion/signal element is moved into detection channel 606 by applying apotential from reservoirs 650 and 652 to reservoirs 658 and 660, whilethe potentials at the remaining reservoirs are allowed to float. Thesubject material regions/signal are then serially moved past thedetection window/detector 662 by applying potentials to reservoirs 654and 656, while applying appropriate potentials at the termini of theother transverse channels to prevent any flow along the various parallelchannels.

Although shown with channels which intersect at right angles, it will beappreciated that other geometries are also appropriate for serial inputparallel reactions. For example, U.S. Ser. No. 08/835,101, filed Apr. 4,1997, describes advantages to parabolic geometries and channels whichvary in width for control of fluid flow. In brief, fluid flow inelectroosmotic systems is controlled by and therefore related to currentflow between electrodes. Resistance in the fluid channels varies as afunction of path length and width, and thus, different length channelshave different resistances. If this differential in resistance is notcorrected for, it results in the creation of transverse electricalfields which can inhibit the ability of the devices to direct fluid flowto particular regions. The current, and thus the fluid flow, follows thepath of least resistance, e.g., the shortest path. While this problem oftransverse electrical fields is alleviated through the use of separateelectrical systems, i.e., separate electrodes, at the termini of eachand every parallel channel, production of devices incorporating all ofthese electrodes, and control systems for controlling the electricalpotential applied at each of these electrodes can be complex,particularly where one is dealing with hundreds to thousands of parallelchannels in a single small scale device, e.g., 1–2 cm². Accordingly, thepresent invention provides microfluidic devices for affecting serial toparallel conversion, by ensuring that current flow through each of aplurality of parallel channels is at an appropriate level to ensure adesired flow pattern through those channels or channel networks. Anumber of methods and substrate/channel designs for accomplishing thesegoals are appropriate.

In one example of parabolic geometry for the channels in an apparatus ofthe invention, the substrate includes a main channel. A series ofparallel channels terminate in a main channel. The opposite termini ofthese parallel channels are connected to parabolic channels. Electrodesare disposed at the termini of these parabolic channels. The currentflow in each of the parallel channels is maintained constant orequivalent, by adjusting the length of the parallel channels, resultingin a parabolic channel structure connecting each of the parallelchannels to its respective electrodes. The voltage drop within theparabolic channel between the parallel channels is maintained constantby adjusting the channel width to accommodate variations in the channelcurrent resulting from the parallel current paths created by theseparallel channels. The parabolic design of the channels, in combinationwith their tapering structures, results in the resistance along all ofthe parallel channels being equal, resulting in an equal fluid flow,regardless of the path chosen. Generally, determining the dimensions ofchannels to ensure that the resistances among the channels arecontrolled as desired, may be carried out by well known methods, andgenerally depends upon factors such as the make-up of the fluids beingmoved through the substrates.

Although generally described in terms of screening assays foridentification of compounds which affect a particular interaction, basedupon the present disclosure, it will be readily appreciated that theabove described microlaboratory systems may also be used to screen forcompounds which specifically interact with a component of a biochemicalsystem without necessarily affecting an interaction between thatcomponent and another element of the biochemical system. Such compoundstypically include binding compounds which may generally be used in,e.g., diagnostic and therapeutic applications as targeting groups fortherapeutics or marker groups, i.e. radionuclides, dyes and the like.For example, these systems are optionally used to screen test compoundsfor the ability to bind to a given component of a biochemical system.

II. Microlaboratory System

Although generally described in terms of individual discrete devices,for ease of operation, the systems described will typically be a part ofa larger system which can monitor and control the functioning of thedevices, either on an individual basis, or in parallel, multi-devicescreens. An example of such a system is shown in FIG. 7.

As shown in FIG. 7, the system may include a test compound processingsystem 700. The system shown includes a platform 702 which can hold anumber of separate assay chips or devices 704. As shown, each chipincludes a number of discrete assay channels 706, each having a separateinterface 708, e.g., pipettor, for introducing test compounds into thedevice. These interfaces are used to sip test compounds into the device,separated by sipping first and second spacer fluids, into the device. Inthe system shown, the interfaces of the chip are inserted through anopening 710 in the bottom of the platform 702, which is capable of beingraised and lowered to place the interfaces in contact with testcompounds or wash/first spacer fluids/second spacer fluids, which arecontained in, e.g., multiwell micro plates 711, positioned below theplatform, e.g., on a conveyor system 712. In operation, multiwell platescontaining large numbers of different test compounds are stacked 714 atone end of the conveyor system. The plates are placed upon the conveyorseparated by appropriate buffer reservoirs 716 and 718, which may befilled by buffer system 720. The plates are stepped down the conveyorand the test compounds are sampled into the chips, interspersed byappropriate spacer fluid regions. After loading the test compounds intothe chips, the multiwell plates are then collected or stacked 722 at theopposite end of the system. The overall control system includes a numberof individual microlaboratory systems or devices, e.g., as shown in FIG.7. Each device is connected to a computer system which is appropriatelyprogrammed to control fluid flow and direction within the various chips,and to monitor, record and analyze data resulting from the screeningassays that are performed by the various devices. The devices willtypically be connected to the computer through an intermediate adaptermodule which provides an interface between the computer and theindividual devices for implementing operational instructions from thecomputer to the devices, and for reporting data from the devices to thecomputer. For example, the adapter will generally include appropriateconnections to corresponding elements on each device, e.g., electricalleads connected to the reservoir based electrodes that are used forelectroosmotic fluid flow, power inputs and data outputs for detectionsystems, either electrical or fiberoptic, and data relays for othersensor elements incorporated into the devices. The adapter device mayalso provide environmental control over the individual devices wheresuch control is necessary, e.g., maintaining the individual devices atoptimal temperatures for performing the particular screening assays.

As shown, each device is also equipped with appropriate fluidinterfaces, e.g., micropipettors, for introducing test compounds intothe individual devices. The devices may readily be attached to roboticsystems which allow test compounds to be sampled from a number ofmultiwell plates that are moved along a conveyor system. Interveningspacer fluid regions can also be introduced via a spacer solutionreservoir.

III. Fluid Electrode Interface to Prevent Degradation of ChemicalSpecies in a Microchip

When pumping fluids or other materials electroosmotically orelectrophoretically through an apparatus of the invention, chemicalspecies in the fluid can be degraded if high voltages or currents areapplied, or if voltages are applied for a long period of time. Designswhich retard movement of chemical species from the electrode to achannel entrance or retard the movement of chemical species to theelectrode improve performance of chemical assays by reducing unwanteddegradation of chemical species within the sample. These designs areparticularly preferred in assay systems where voltages are applied forlong periods, e.g., several hours to several days.

Electrode designs which reduce degradation of chemical species in theassays of the invention are illustrated by consideration of FIG. 12,panels A–G. The designs retard the moving of chemical species from theelectrode to the channel entrance or retard the movement of chemicalspecies to the electrode improve performance of chemical assays. FIG.12A shows a typical electrode design, in which electrode 1211 ispartially submerged in reservoir 1215 fluidly connected to fluid channel1217.

In comparison, FIG. 12B utilizes a salt bridge between electrode withfrit 1219 and fluid reservoir 1221 fluidly connected to fluid channel1223.

FIG. 12C reduces degradation of chemical species by providing electrode1225 submersed in first fluid reservoir 1227 fluidly connected to secondfluid reservoir 1229 by large channel 1231 which limits diffusion, buthas a low electroosmotic flow.

FIG. 12D provides a similar two part reservoir, in which electrode 1235is submersed in first fluid reservoir 1237 fluidly connected to secondfluid reservoir 1241 by small channel 1243 which is treated to reduce oreliminate electroosmotic flow.

FIG. 12E provides another similar two part reservoir, in which electrode1245 is submersed in first fluid reservoir 1247 fluidly connected tosecond fluid reservoir 1251 by channel 1253. Channel 1253 is filled witha material such as gel, Agar, glass beads or other matrix material forreducing electroosmotic flow.

FIG. 12F provides a variant two part reservoir system, in whichelectrode 1255 is submersed in first fluid reservoir 1257 fluidlyconnected to second fluid reservoir 1259 by channel 1261. The fluidlevel in second fluid reservoir 1259 is higher than the fluid level infirst fluid reservoir 1257, which forces fluid towards electrode 1255.

FIG. 12G provides a second variant two part reservoir, in whichelectrode 1265 is submersed in first fluid reservoir 1267 fluidlyconnected to second fluid reservoir 1269 by channel 1271. The diameteron first fluid reservoir 1267 is small enough that capillary forces drawfluid into first fluid reservoir 1267.

Modifications can be made to the method and apparatus as hereinbeforedescribed without departing from the spirit or scope of the invention asclaimed, and the invention can be put to a number of different uses,including:

The use of a microfluidic system containing at least a first substratehaving a first channel and a second channel intersecting said firstchannel, at least one of said channels having at least onecross-sectional dimension in a range from 0.1 to 500 μm, in order totest the effect of each of a plurality of test compounds on abiochemical system.

The use of a microfluidic system as hereinbefore described, wherein saidbiochemical system flows through one of said channels substantiallycontinuously, enabling sequential testing of said plurality of testcompounds.

The use of a microfluidic system as hereinbefore described, wherein theprovision of a plurality of reaction channels in said first substrateenables parallel exposure of a plurality of test compounds to at leastone biochemical system.

The use of a microfluidic system as hereinbefore described, wherein eachtest compound is physically isolated from adjacent test compounds.

The use of a substrate carrying intersecting channels in screening testmaterials for effect on a biochemical system by flowing said testmaterials and biochemical system together using said channels.

The use of a substrate as hereinbefore described, wherein at least oneof said channels has at least one cross-sectional dimension of range 0.1to 500 μm.

An assay utilizing a use of any one of the microfluidic systems orsubstrates hereinbefore described.

The invention provides, inter alia, an apparatus for detecting an effectof a test compound on a biochemical system, comprising a substratehaving at least one surface with a plurality of reaction channelsfabricated into the surface. Apparatus as hereinbefore described, havingat least two transverse channels fabricated into the surface, whereineach of the plurality of reaction channels is fluidly connected to afirst of the at least two transverse channels at a first point in eachof the reaction channels, and fluidly connected to a second transversechannel at a second point in each of the reaction channels and an assayapparatus including an apparatus as hereinbefore described are alsoprovided.

EXAMPLES

The following examples are provided by way of illustration only and notby way of limitation. Those of skill will readily recognize a variety ofnoncritical parameters which can be changed or modified to yieldessentially similar results.

Example 1 Enzyme Inhibitor Screen

The efficacy of performing an enzyme inhibition assay screen wasdemonstrated in a planar chip format. A 6-port planar chip was employedhaving the layout shown in FIG. 8. The numbers adjacent the channelsrepresent the lengths of each channel in millimeters. Two voltage stateswere applied to the ports of the chip. The first state (State 1)resulted in flowing of enzyme with buffer from the top buffer well intothe main channel. The second voltage state (State 2) resulted in theinterruption of the flow of buffer from the top well, and theintroduction of inhibitor from the inhibitor well, into the main channelalong with the enzyme. A control experiment was also run in which bufferwas placed into the inhibitor well.

Applied voltages at each port for each of the two applied voltage stateswere as follows:

State 1 State 2 Top Buffer Well (I) 1831 1498 Inhibitor Well (II) 14981900 Enzyme Well (III) 1891 1891 Substrate Well (IV) 1442 1442 BottomBuffer Well (V) 1442 1442 Detect./Waste Well (VI) 0 0

To demonstrate the efficacy of the system, an assay was designed toscreen inhibitors of β-galactosidase using the followingenzyme/substrate/inhibitor reagents:

Enzyme: β-Galactosidase (180 U/ml in 50 mM Tris/300 μg/ml BSA Substrate:Fluorescein-digalactoside (FDG) 400 μM Inhibitor: IPTG, 200 mM Buffer:20 mM Tris, pH 8.5Enzyme and substrate were continually pumped through the main channelfrom their respective ports under both voltage states. Inhibitor orBuffer were delivered into the main channel alternately from theirrespective wells by alternating between voltage state 1 and voltagestate 2. When no inhibitor was present at the detection end of the mainchannel, a base line level of fluorescent product was produced. Uponintroduction of inhibitor, the fluorescent signal was greatly reduced,indicating inhibition of the enzyme/substrate interaction. Fluorescentdata obtained from the alternating delivery of inhibitor and buffer intothe main channel is shown in FIG. 9A. FIG. 9B a superposition of the twodata segments from FIG. 9A, directly comparing the inhibitor data withcontrol (buffer) data. The control shows only a minor fluctuation in thefluorescent signal that apparently resulted from a dilution of theenzyme substrate mixture, whereas the inhibitor screen shows asubstantial reduction in the fluorescent signal, indicating clearinhibition.

Example 2 Screening of Multiple Test Compounds

An assay screen is performed to identify inhibitors of an enzymaticreaction. A schematic of the chip to be used is shown in FIG. 10. Thechip has a reaction channel 5 cm in length which includes a 1 cmincubation zone and a 4 cm reaction zone. The reservoir at the beginningof the sample channel is filled with enzyme solution and the sidereservoir is filled with the fluorogenic substrate. Each of the enzymeand substrate are diluted to provide for a steady state signal in thelinear signal range for the assay system, at the detector. Potentialsare applied at each of the reservoirs (sample source, enzyme, substrateand waste) to achieve an applied field of 200 V/cm. This applied fieldproduces a flow rate of 2 mm/second. During passage of a given samplethrough the chip, there will generally be a diffusive broadening of thesample. For example, in the case of a small molecule sample, e.g., 1 mMbenzoic acid diffusive broadening of approximately 0.38 mm and anelectrophoretic shift of 0.4 mm is seen.

Subject material regions containing test compounds in 150 mM NaCl areintroduced into the sample channel separated by first spacer regions of150 mM NaCl and second spacer regions of 5 mM borate buffer. Onceintroduced into the sample channel shown, the subject material regionrequires 12 seconds to travel the length of the sample channel and reachthe incubation zone of the reaction channel. This is a result of theflow rate of 2 mm/sec, allowing for 1 second for moving the samplepipettor from the sample to the spacer compounds. Allowing for theseinterruptions, the net flow rate is 0.68 mm/sec. Another 12 seconds isrequired for the enzyme/test compound mixture to travel through theincubation zone to the intersection with the substrate channel wheresubstrate is continuously flowing into the reaction zone of the reactionchannel. Each subject material region containing the test compounds thenrequires 48 seconds to travel the length of the reaction zone and pastthe fluorescence detector. A schematic of timing for subject materialregion/spacer region loading is shown in FIG. 11. The top panel showsthe subject material/first spacer region/second spacer regiondistribution within a channel, whereas the lower panel shows the timingrequired for loading the channel. As shown, the schematic includes theloading (sipping) of high salt (HS) first spacer fluid (“A”), moving thepipettor to the sample or subject material (“B”), sipping the sample orsubject material (“C”), moving the pipettor to the high salt firstspacer fluid (“D”) sipping the first spacer fluid (“E”), moving thepipettor to the low salt (LS) or second spacer fluid (“F”), sipping thesecond spacer fluid (“G”) and returning to the first spacer fluid (“H”).The process is then repeated for each additional test compound.

A constant base fluorescent signal is established at the detector in theabsence of test compounds. Upon introduction of the test compounds, adecrease in fluorescence is seen similar to that shown in FIGS. 9A and9B, which, based upon time delays, corresponds to a specific individualtest compound. This test compound is tentatively identified as aninhibitor of the enzyme, and further testing is conducted to confirmthis and quantitate the efficacy of this inhibitor.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. All publications and patent documents cited in thisapplication are incorporated by reference in their entirety for allpurposes to the same extent as if each individual publication or patentdocument were so individually denoted.

1. A method of screening one or more test compounds for an effect on atleast one cell using an analytical device comprising: flowing one ormore test compounds from one or more test compound sources through oneor more microfluidic channels of an analytical device fabricated in aplanar substrate, wherein the one more microfluidic channels have atleast one cross-sectional dimension in a range from about 0.1 to 500 μm;contacting the one or more test compounds with at least a first cell;and detecting a cellular response of the at least first cell to the oneor more test compounds in a detection zone of the device, wherein thecellular response is selected from the group consisting of cellproliferation, cell differentiation, cell activation, activation of acell activity mediating enzyme, stimulation of messenger turnover in thecell, alteration of cell ion flux, activation of cellular enzymes,changes in cell shape, and an alteration in expression of a gene.
 2. Themethod of claim 1, wherein the one or more test compounds comprise aplurality of test compounds which are each fluidly coupled to arespective test compound source.
 3. The method of claim 2, wherein theone or more microfluidic channels comprises at least 10 microfluidicchannels.
 4. The method of claim 2, wherein the one or more microfluidicchannels comprises between 10 to about 500 microfluidic channels.
 5. Themethod of claim 1, wherein the at least first cell is isolated from anin vitro source.
 6. The method of claim 1, wherein the at least firstcell is isolated from an in viva source.
 7. The method of claim 1,wherein to at least first cell is selected from the group consisting ofa bacterial cell, a plant cell, a fungal cell, and an animal cell. 8.The method of claim 1, wherein a pressure based fluid direction systemis used for flowing said one or more test compounds within said one ormore microfluidic channels.
 9. The method of claim 1, wherein anelectrokinetic fluid direction system is used for flowing said one ormore test compounds within said one or more microfluidic channels. 10.The method of claim 1, wherein the analytical device comprises or isconnectable to a computer so that the computer controls the device. 11.The method of claim 10, wherein the computer controls fluid flow anddirection within the device.
 12. The method of claim 10, wherein thecomputer is connected to the device via an adaptor module which providesenvironmental control over the device.
 13. The method of claim 1,further comprising a fluid interface for introducing the one or moretest compounds into the device.
 14. The method of claim 13, wherein thefluid interface is one or more micropipettors.
 15. The method of claim1, wherein the one or more test compounds comprise a plurality of testcompounds which are each contained within a separate reservoir of theanalytical device.
 16. The method of claim 15, further comprisingtransporting the plurality of test compounds from the separatereservoirs into a plurality of respective microfluidic channels using apressure-based fluid direction system.
 17. A method of screening one ormore test compounds for an effect on at least one cell using ananalytical device comprising: flowing one or more test compounds fromone or more test compound sources through one or more microfluidicchannels of an analytical device fabricated in a planar substrate,wherein the one more microfluidic channels have at least onecross-sectional dimension in a range from about 0.1 to 500 μm;contacting the one or more test compounds with at least a first cell;and detecting a cellular response of the at least first cell to the oneor more test compounds in a detection zone of to device, wherein themethod is for characterizing one or mare receptors present in the atleast first cell, wherein the one or more test compounds have an effecton at least one of the one or more receptors in the at least first cell.18. A method of screening one or more test compounds for an effect on atleast one cell using an analytical device comprising: flowing one ormore test compounds from one or more test compound sources through oneor more microfluidic channels of an analytical device fabricated in aplanar substrate, wherein the one more microfluidic channels have atleast one cross-sectional dimension in a range from about 0.1 to 500 μm;contacting the one or more test compounds with at least a first cell;and detecting a cellular response of the at least first cell to the oneor more test compounds in a detection zone of the device, wherein thedetection zone is configured to be coupled to a detector for measuringan effect of the one or more test compounds on the at least first cellby measuring a level of a detectable signal, and wherein the detectablesignal is provided by a label or a change in molecular weight.
 19. Themethod of claim 18, wherein the detectable signal results from an effectof the one or more test compounds on a cellular function of the at leastfirst cell.
 20. The method of claim 19, wherein the cellular function iscellular viability or cellular activity.
 21. The method of claim 18,wherein the label is a chromophoric label or a fluorescent label. 22.The method of claim 18, wherein the detectable signal is radioactivedecay, electron density, change in pH, temperature or saltconcentration.
 23. The method of claim 18, wherein the cellular responsecomprises alteration in cell ion flux.